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(-) Description

Title :  STRUCTURE OF APPBP1-UBA3~NEDD8-NEDD8-MGATP-UBC12(C111A), A TRAPPED UBIQUITIN-LIKE PROTEIN ACTIVATION COMPLEX
 
Authors :  D. T. Huang, H. W. Hunt, M. Zhuang, M. D. Ohi, J. M. Holton, B. A. Schulman
Date :  13 Nov 06  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,I,J
Keywords :  Multifunction Macromolecular Complex, Ubiquitin, Nedd8, E1, E2, Atp, Conformational Change, Thioester, Switch, Adenylation, Protein Turnover, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. T. Huang, H. W. Hunt, M. Zhuang, M. D. Ohi, J. M. Holton, B. A. Schulman
Basis For A Ubiquitin-Like Protein Thioester Switch Toggling E1-E2 Affinity.
Nature V. 445 394 2007
PubMed-ID: 17220875  |  Reference-DOI: 10.1038/NATURE05490
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEDD8-ACTIVATING ENZYME E1 REGULATORY SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T-1
    Expression System StrainBL21(DE3)GOLD
    Expression System Taxid562
    Expression System VectorBICISTRONIC PGEX4T-3 DERIVATIVE
    Expression System Vector TypePLASMID
    GeneAPPBP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAMYLOID PROTEIN-BINDING PROTEIN 1, AMYLOID BETA PRECURSOR PROTEIN-BINDING PROTEIN 1, 59 KDA, APP-BP1, PROTOONCOGENE PROTEIN 1, HPP1
 
Molecule 2 - MALTOSE BINDING PROTEIN/NEDD8-ACTIVATING ENZYME E1 CATALYTIC SUBUNIT CHIMERA
    ChainsB
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T-1
    Expression System StrainBL21(DE3)GOLD
    Expression System Taxid562
    Expression System VectorBICISTRONIC PGEX4T-3 DERIVATIVE
    Expression System Vector TypePLASMID
    FragmentRESIDUES 33-463
    GeneUBE1C, UBA3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsFUSION PROTEIN. MALTOSE BINDING PROTEIN (RESIDUES 1001-1371), AND THE NEDD8-ACTIVATING ENZYME E1 CATALYTIC SUBUNIT (RESIDUES 2012-2442) IS FROM A HUMAN SOURCE
    SynonymMBP, UBIQUITIN-ACTIVATING ENZYME 3, NEDD8- ACTIVATING ENZYME E1C, UBIQUITIN-ACTIVATING ENZYME E1C
 
Molecule 3 - NEDD8-CONJUGATING ENZYME UBC12
    ChainsC
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T-1
    Expression System StrainBL21(DE3)GOLD
    Expression System Taxid562
    Expression System VectorBICISTRONIC PGEX4T-3 DERIVATIVE
    Expression System Vector TypePLASMID
    GeneUBE2M, UBC12
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-CONJUGATING ENZYME E2 M, NEDD8 PROTEIN LIGASE, NEDD8 CARRIER PROTEIN
 
Molecule 4 - NEDD8
    ChainsI, J
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T-1
    Expression System StrainBL21(DE3)GOLD
    Expression System Taxid562
    Expression System VectorBICISTRONIC PGEX4T-3 DERIVATIVE
    Expression System Vector TypePLASMID
    GeneNEDD8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-LIKE PROTEIN NEDD8, NEDDYLIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:45 , ATP B:103 , ASP B:2146BINDING SITE FOR RESIDUE MG B 101
2AC2SOFTWARECYS B:2199 , CYS B:2202 , CYS B:2343 , CYS B:2346BINDING SITE FOR RESIDUE ZN B 102
3AC3SOFTWAREARG A:15 , HOH B:5 , HOH B:31 , HOH B:40 , HOH B:45 , MG B:101 , ALA B:2056 , GLY B:2057 , ASP B:2079 , MET B:2080 , ASP B:2081 , ASN B:2087 , ARG B:2090 , GLN B:2091 , LYS B:2103 , ASN B:2125 , LYS B:2126 , ILE B:2127 , GLN B:2128 , GLY B:2144 , ASP B:2146 , GLY I:76BINDING SITE FOR RESIDUE ATP B 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NVU)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr C:86 -Pro C:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052435S101FULA1_HUMANPolymorphism363212AS101F
2UniProtVAR_023945K9RUBA3_HUMANPolymorphism17852113BI1330R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (6, 8)

Asymmetric/Biological Unit (6, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.NEDD8_HUMAN1-76
 
  2I:1-76
J:1-76
2UBIQUITIN_1PS00299 Ubiquitin domain signature.NEDD8_HUMAN27-52
 
  2I:27-52
J:27-52
3UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBC12_HUMAN32-162  1C:32-162
4UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBC12_HUMAN100-115  1C:100-115
5SBP_BACTERIAL_1PS01037 Bacterial extracellular solute-binding proteins, family 1 signature.MALE_ECOLI133-150  1B:1108-1125
6UBIQUITIN_ACTIVAT_2PS00865 Ubiquitin-activating enzyme active site.UBA3_HUMAN235-243  1B:2214-2222

(-) Exons   (48, 52)

Asymmetric/Biological Unit (48, 52)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002504951aENSE00001101093chr14:24701660-24701456205NEDD8_HUMAN1-662I:1-6
J:1-6
6
6
1.4ENST000002504954ENSE00002175755chr14:24687637-2468759048NEDD8_HUMAN7-22162I:7-22
J:7-22
16
16
1.5aENST000002504955aENSE00002178617chr14:24687421-2468733983NEDD8_HUMAN23-50282I:23-50
J:23-50
28
28
1.6eENST000002504956eENSE00001549615chr14:24686429-24686058372NEDD8_HUMAN50-81322I:50-76
J:50-76
27
27

2.1ENST000002530231ENSE00000892667chr19:59070343-59069640704UBC12_HUMAN1-37371C:3-37 (gaps)35
2.2ENST000002530232ENSE00000655803chr19:59068524-5906843095UBC12_HUMAN37-68321C:37-6832
2.3ENST000002530233ENSE00000655805chr19:59068297-5906825939UBC12_HUMAN69-81131C:69-8113
2.4ENST000002530234ENSE00000655806chr19:59068157-59068054104UBC12_HUMAN82-116351C:82-11635
2.5ENST000002530235ENSE00000655807chr19:59067746-5906768364UBC12_HUMAN116-137221C:116-13722
2.6ENST000002530236ENSE00000892668chr19:59067596-59067080517UBC12_HUMAN138-183461C:138-18346

3.1aENST000002908101aENSE00001857882chr16:66864900-66864750151ULA1_HUMAN1-18181A:5-1814
3.3aENST000002908103aENSE00001739042chr16:66860683-66860580104ULA1_HUMAN18-53361A:18-5336
3.4ENST000002908104ENSE00001779668chr16:66860486-6686042661ULA1_HUMAN53-73211A:53-7321
3.5ENST000002908105ENSE00001624314chr16:66858788-6685875831ULA1_HUMAN73-83111A:73-8311
3.6ENST000002908106ENSE00001761968chr16:66857503-6685743272ULA1_HUMAN84-107241A:84-10724
3.7ENST000002908107ENSE00001104193chr16:66857209-6685713080ULA1_HUMAN108-134271A:108-13427
3.8ENST000002908108ENSE00001104205chr16:66855462-66855353110ULA1_HUMAN134-171381A:134-17138
3.9ENST000002908109ENSE00001104202chr16:66852540-66852431110ULA1_HUMAN171-207371A:171-20737
3.10ENST0000029081010ENSE00001104208chr16:66851390-6685132863ULA1_HUMAN208-228211A:208-22821
3.11ENST0000029081011ENSE00001104214chr16:66850931-6685086864ULA1_HUMAN229-250221A:229-25022
3.12ENST0000029081012ENSE00001104186chr16:66850575-6685048492ULA1_HUMAN250-280311A:250-28031
3.13ENST0000029081013ENSE00001139971chr16:66847749-6684769060ULA1_HUMAN281-300201A:281-30020
3.14ENST0000029081014ENSE00001139961chr16:66847600-66847467134ULA1_HUMAN301-345451A:301-34545
3.15ENST0000029081015ENSE00001139952chr16:66844675-6684460076ULA1_HUMAN345-370261A:345-37026
3.16ENST0000029081016ENSE00001046614chr16:66844316-6684427740ULA1_HUMAN371-384141A:371-38414
3.17ENST0000029081017ENSE00001046603chr16:66842978-6684289287ULA1_HUMAN384-413301A:384-41330
3.18ENST0000029081018ENSE00001046627chr16:66842516-6684242493ULA1_HUMAN413-444321A:413-44432
3.19ENST0000029081019ENSE00001104192chr16:66839929-66839815115ULA1_HUMAN444-482391A:444-48239
3.20ENST0000029081020ENSE00001104217chr16:66839729-6683968050ULA1_HUMAN482-499181A:482-49918
3.21bENST0000029081021bENSE00001907559chr16:66837021-66836778244ULA1_HUMAN499-534361A:499-53436

4.1aENST000003610551aENSE00001864869chr3:69129559-6912948575UBA3_HUMAN1-771B:1322-13287
4.2aENST000003610552aENSE00001417479chr3:69129304-6912926342UBA3_HUMAN7-21151B:1328-135528
4.3aENST000003610553aENSE00000966869chr3:69127069-69126949121UBA3_HUMAN21-61411B:1355-2040 (gaps)47
4.4aENST000003610554aENSE00001377164chr3:69124661-6912458181UBA3_HUMAN62-88271B:2041-206727
4.5aENST000003610555aENSE00001376644chr3:69120768-6912068683UBA3_HUMAN89-116281B:2068-209528
4.6ENST000003610556ENSE00000966872chr3:69117159-6911707981UBA3_HUMAN116-143281B:2095-212228
4.7aENST000003610557aENSE00000966873chr3:69113262-6911321944UBA3_HUMAN143-158161B:2122-213716
4.8ENST000003610558ENSE00000966874chr3:69112654-6911259065UBA3_HUMAN158-179221B:2137-215822
4.9ENST000003610559ENSE00000966875chr3:69112288-69112133156UBA3_HUMAN180-231521B:2159-221052
4.10ENST0000036105510ENSE00000966876chr3:69111330-69111228103UBA3_HUMAN232-266351B:2211-224535
4.11aENST0000036105511aENSE00000966877chr3:69111078-69110965114UBA3_HUMAN266-304391B:2245-228339
4.12ENST0000036105512ENSE00000966878chr3:69106460-6910640754UBA3_HUMAN304-322191B:2283-230119
4.13ENST0000036105513ENSE00001656120chr3:69105966-6910593037UBA3_HUMAN322-334131B:2301-231313
4.14ENST0000036105514ENSE00001685710chr3:69105844-6910576382UBA3_HUMAN334-361281B:2313-234028
4.15ENST0000036105515ENSE00001754233chr3:69105434-69105334101UBA3_HUMAN362-395341B:2341-237434
4.16ENST0000036105516ENSE00001711956chr3:69105214-6910515164UBA3_HUMAN395-416221B:2374-239522
4.17ENST0000036105517ENSE00001673741chr3:69105056-6910500255UBA3_HUMAN417-435191B:2396-241419
4.18bENST0000036105518bENSE00001518240chr3:69104676-69103881796UBA3_HUMAN435-463291B:2414-244229

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:530
 aligned with ULA1_HUMAN | Q13564 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:530
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534
          ULA1_HUMAN      5 GKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL  534
               SCOP domains d2nvua_ A: Amyloid beta precursor protein-binding protein 1, APPBP1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2nvuA01 A:5-178,A:388-534 NAD(P)-binding Rossmann-like Domain                                                                                                                 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2nvuA01 A:5-178,A:388-534 NAD(P)-binding Rossmann-like Domain                                                                                       CATH domains
               Pfam domains ------------------------ThiF-2nvuA01 A:29-165                                                                                                                    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh....eeeee.....hhhhhhh....hhhhh..hhhhhhhhhhh......eeeee..hhhhhhhhh.hhhhh..eeeee..hhhhhhhhhhhhhhh...eeeeeee..eeeeeee...eee.................hhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh............hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhheee...hhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......eeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 3 (1) Exon 3.1a     ----------------------------------Exon 3.4  PDB: A:53-7----------Exon 3.6  PDB: A:84-107 Exon 3.7  PDB: A:108-134   ------------------------------------Exon 3.9  PDB: A:171-207             Exon 3.10            Exon 3.11             ------------------------------Exon 3.13           Exon 3.14  PDB: A:301-345 UniProt: 301-345   -------------------------Exon 3.16     ----------------------------Exon 3.18  PDB: A:413-444       -------------------------------------Exon 3.20         ----------------------------------- Transcript 3 (1)
           Transcript 3 (2) -------------Exon 3.3a  PDB: A:18-53             -------------------Exon 3.5   --------------------------------------------------Exon 3.8  PDB: A:134-171              ------------------------------------------------------------------------------Exon 3.12  PDB: A:250-280      ----------------------------------------------------------------Exon 3.15  PDB: A:345-370 -------------Exon 3.17  PDB: A:384-413     ------------------------------Exon 3.19  PDB: A:444-482              ----------------Exon 3.21b  PDB: A:499-534           Transcript 3 (2)
                2nvu A    5 GKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL  534
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534

Chain B from PDB  Type:PROTEIN  Length:789
 aligned with MALE_ECOLI | P0AEX9 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:801
                                                                                                                                                                                                                                                                                                                                                                                                                      396                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                       392         393  |                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386     |   -       395|        -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         - 
          MALE_ECOLI     27 KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQT-----------RITK------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------    -
               SCOP domains d2nvub2 B:1002-1367 D-maltodextrin-binding protein, MBP                                                                                                                                                                                                                                                                                                                       ----d2nvub1 B:2012-2441 UBA3                                                                                                                                                                                                                                                                                                                                                                                                                      - SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ThiF-2nvuB01 B:2047-2192                                                                                                                          --UBA_e1_thiolCys-2nvuB04 B:2195-2241            ------UBACT-2nvuB03 B:2248-2314                                          --------------------------------------E2_bind-2nvuB02 B:2353-2441                                                              - Pfam domains
         Sec.struct. author ......eeee......hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhh.....eeeeehhhhhhhhhhh.......hhhhhh....hhhhhhee..ee.eeeeeeee.eeee.............hhhhhhhhhhh...eee.....hhhhhhhhhhh...eeeee....eeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh...eeeeee...............................eeeeeeee......hhhhhhhhhh...hhhhhhhhhh..----..hhhhhh.--------hhhhhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhh............hhhhhhhhhh..eeee...hhhhhhhhhhhh....eeeeee....hhhhhhh....hhhhh..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..ee..ee.hhhh..eeeeeee..eeeeeee..........hhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee...............eeeee....hhhhhhhhhhhh........eeeeee..eeeeee...hhhhhhhhhhhhhh...........eeeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------SBP_BACTERIAL_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2nvu B 1002 KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDK----VALKSYEEE--------ATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAADWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS 2442
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      |  - |    1311      1321      1331      1341      1351      1361      1371|     2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241      2251      2261      2271      2281      2291      2301      2311      2321      2331      2341      2351      2361      2371      2381      2391      2401      2411      2421      2431      2441 
                                                                                                                                                                                                                                                                                                                                 1298 1303    1311     1320                                               1371|                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                           2012                                                                                                                                                                                                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:789
 aligned with UBA3_HUMAN | Q8TBC4 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:789
                                                                                                                                                                                                                                                                                                                                                1       10            11                   32    33                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -        |2       | -         - |      19        29  |     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454         
          UBA3_HUMAN      - --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MADGEEPEKK-------------RRRIEELLAEKMAVDGGCGDTG-----DWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS  463
               SCOP domains d2nvub2 B:1002-1367 D-maltodextrin-binding protein, MBP                                                                                                                                                                                                                                                                                                           ----d2nvub1 B:2012-2441 UBA3                                                                                                                                                                                                                                                                                                                                                                                                                      - SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ThiF-2nvuB01 B:2047-2192                                                                                                                          --UBA_e1_thiolCys-2nvuB04 B:2195-2241            ------UBACT-2nvuB03 B:2248-2314                                          --------------------------------------E2_bind-2nvuB02 B:2353-2441                                                              - Pfam domains
         Sec.struct. author ......eeee......hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhh.....eeeeehhhhhhhhhhh.......hhhhhh....hhhhhhee..ee.eeeeeeee.eeee.............hhhhhhhhhhh...eee.....hhhhhhhhhhh...eeeee....eeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhh...eeeeee...............................eeeeeeee......hhhhhhhhhh...hhhhhhhhhh....hhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhh............hhhhhhhhhh..eeee...hhhhhhhhhhhh....eeeeee....hhhhhhh....hhhhh..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..ee..ee.hhhh..eeeeeee..eeeeeee..........hhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee...............eeeee....hhhhhhhhhhhh........eeeeee..eeeeee...hhhhhhhhhhhhhh...........eeeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBIQUITIN---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 4 (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------4.1a   --------------------------Exon 4.3a  PDB: B:1355-2040 (gaps)            Exon 4.4a  PDB: B:2041-2067Exon 4.5a  PDB: B:2068-2095 --------------------------Exon 4.7a       ---------------------Exon 4.9  PDB: B:2159-2210 UniProt: 180-231         Exon 4.10  PDB: B:2211-2245        -------------------------------------Exon 4.12          -----------Exon 4.14  PDB: B:2313-2340 Exon 4.15  PDB: B:2341-2374       ---------------------Exon 4.17          ---------------------------- Transcript 4 (1)
           Transcript 4 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 4.2a  PDB: B:1328-1355 ---------------------------------------------------------------------------------------------------Exon 4.6  PDB: B:2095-2122  --------------Exon 4.8              --------------------------------------------------------------------------------------Exon 4.11a  PDB: B:2245-2283           -----------------Exon 4.13    ------------------------------------------------------------Exon 4.16             ------------------Exon 4.18b  PDB: B:2414-2442  Transcript 4 (2)
                2nvu B 1002 KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKVALKSYEEEATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAADWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS 2442
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1305     |1323      1333      1343      1353      1363      2013      2023      2033      2043      2053      2063      2073      2083      2093      2103      2113      2123      2133      2143      2153      2163      2173      2183      2193      2203      2213      2223      2233      2243      2253      2263      2273      2283      2293      2303      2313      2323      2333      2343      2353      2363      2373      2383      2393      2403      2413      2423      2433         
                                                                                                                                                                                                                                                                                                                                 1298|    1311|                                               1371|                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                  1303     1320                                                2012                                                                                                                                                                                                                                                                                                                                                                                                                                              

Chain C from PDB  Type:PROTEIN  Length:176
 aligned with UBC12_HUMAN | P61081 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 
         UBC12_HUMAN      3 KLFSLKQQKKEEESAGGTKGSSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGFYKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPNIDLEGNVCLNILREDWKPVLTINSIIYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQRSMRGGYIGSTYFERCLK  183
               SCOP domains d2nvuc1 C:3-1     83 Ubiquitin conjugating enzyme, UBC                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------UQ_con-2nvuC01 C:33-168                                                                                                                 --------------- Pfam domains
         Sec.struct. author .............-----.......hhhhhhhhhhhhh......eeee........eeeeee...hhhhh...eeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhheee..eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------UBIQUITIN_CONJUGAT_2  PDB: C:32-162 UniProt: 32-162                                                                                --------------------- PROSITE (3)
                PROSITE (1) -------------------------------------------------------------------------------------------------UBIQUITIN_CONJUG-------------------------------------------------------------------- PROSITE (1)
           Transcript 2 (1) Exon 2.1  PDB: C:3-37 (gaps)       -------------------------------Exon 2.3     Exon 2.4  PDB: C:82-116            ---------------------Exon 2.6  PDB: C:138-183 UniProt: 138-183      Transcript 2 (1)
           Transcript 2 (2) ----------------------------------Exon 2.2  PDB: C:37-68          -----------------------------------------------Exon 2.5              ---------------------------------------------- Transcript 2 (2)
                2nvu C    3 KLFSLKQQKKEEE-----KGSSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGFYKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPNIDLEGNVALNILREDWKPVLTINSIIYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQRSMRGGYIGSTYFERCLK  183
                                    12  |     22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 
                                       15    21                                                                                                                                                                  

Chain I from PDB  Type:PROTEIN  Length:76
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:76
                                    10        20        30        40        50        60        70      
         NEDD8_HUMAN      1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG   76
               SCOP domains d2nvui_ I: Nedd8                                                             SCOP domains
               CATH domains 2nvuI00 I:1-76                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhh.eee..ee................eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: I:1-76 UniProt: 1-76                                       PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: I:27-52 ------------------------ PROSITE (2)
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: I:23-50     -------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: I:50-76     Transcript 1 (2)
                2nvu I    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG   76
                                    10        20        30        40        50        60        70      

Chain J from PDB  Type:PROTEIN  Length:76
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:76
                                    10        20        30        40        50        60        70      
         NEDD8_HUMAN      1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG   76
               SCOP domains d2nvuj_ J: Nedd8                                                             SCOP domains
               CATH domains 2nvuJ00 J:1-76                                                               CATH domains
           Pfam domains (1) -----ubiquitin-2nvuJ01 J:6-74                                             -- Pfam domains (1)
           Pfam domains (2) -----ubiquitin-2nvuJ02 J:6-74                                             -- Pfam domains (2)
         Sec.struct. author ..eeeee...eeee........hhhhhhhhh..........eee..........hhhhhh....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: J:1-76 UniProt: 1-76                                       PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: J:27-52 ------------------------ PROSITE (2)
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: J:23-50     -------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: J:50-76     Transcript 1 (2)
                2nvu J    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG   76
                                    10        20        30        40        50        60        70      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (5, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (6, 8)

Asymmetric/Biological Unit
(-)
Family: ThiF (14)
1aThiF-2nvuB01B:2047-2192
1bThiF-2nvuA01A:29-165
(-)
Clan: UBC (69)
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (58, 86)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ULA1_HUMAN | Q13564)
molecular function
    GO:0019781    NEDD8 activating enzyme activity    Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0008641    small protein activating enzyme activity    Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0033314    mitotic DNA replication checkpoint    A cell cycle checkpoint that acts during a mitotic cell cycle and prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0043523    regulation of neuron apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (MALE_ECOLI | P0AEX9)
molecular function
    GO:1901982    maltose binding    Interacting selectively and non-covalently with maltose.
    GO:0005363    maltose transmembrane transporter activity    Enables the transfer of maltose from one side of the membrane to the other. Maltose is the disaccharide 4-O-alpha-D-glucopyranosyl-D-glucopyranose, an intermediate in the enzymatic breakdown of glycogen and starch.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0034289    detection of maltose stimulus    The series of events in which a maltose stimulus is received by a cell and converted into a molecular signal.
    GO:0042956    maltodextrin transport    The directed movement of maltodextrin, any polysaccharide of glucose residues in beta-(1,4) linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015768    maltose transport    The directed movement of maltose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Maltose is the disaccharide 4-O-alpha-D-glucopyranosyl-D-glucopyranose, an intermediate in the catabolism of glycogen and starch.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    GO:0055052    ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing    A complex for the transport of metabolites into the cell, consisting of 5 subunits: two ATP-binding subunits, two membrane spanning subunits, and one substrate-binding subunit. In organisms with two membranes, the substrate-binding protein moves freely in the periplasmic space and joins the other subunits only when bound with substrate. In organisms with only one membrane the substrate-binding protein is tethered to the cytoplasmic membrane and associated with the other subunits. Transport of the substrate across the membrane is driven by the hydrolysis of ATP.
    GO:1990060    maltose transport complex    Protein complex facilitating ATP-dependent maltose transport through inner cell membrane (periplasm to cytoplasm) in Gram-negative bacteria. In E. coli the system is composed of a periplasmic maltose-binding protein (MBP), two integral membrane proteins, MalF and MalG, and two copies of the cytoplasmic ATP-binding cassette MalK.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain B   (UBA3_HUMAN | Q8TBC4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019781    NEDD8 activating enzyme activity    Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade.
    GO:0016881    acid-amino acid ligase activity    Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0008641    small protein activating enzyme activity    Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
biological process
    GO:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0007113    endomitotic cell cycle    A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain C   (UBC12_HUMAN | P61081)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019788    NEDD8 transferase activity    Catalysis of the transfer of NEDD8 from one protein to another via the reaction X-NEDD8 + Y --> Y-NEDD8 + X, where both X-NEDD8 and Y-NEDD8 are covalent linkages.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0018169    ribosomal S6-glutamic acid ligase activity    Catalysis of the posttranslational transfer of one or more glutamic acid residues to the C-terminus of ribosomal protein S6.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Chain I,J   (NEDD8_HUMAN | Q15843)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MALE_ECOLI | P0AEX91a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2d21 2h25 2klf 2mv0 2n44 2n45 2obg 2ok2 2r6g 2v93 2vgq 2xz3 2zxt 3a3c 3c4m 3csb 3csg 3d4c 3d4g 3dm0 3ef7 3ehs 3eht 3ehu 3f5f 3g7v 3g7w 3h3g 3h4z 3hpi 3hst 3io4 3io6 3ior 3iot 3iou 3iov 3iow 3j9p 3kjt 3l2j 3lbs 3lc8 3mbp 3mp1 3mp6 3mp8 3mq9 3n94 3o3u 3oai 3osq 3osr 3pgf 3puv 3puw 3pux 3puy 3puz 3pv0 3py7 3q25 3q26 3q27 3q28 3q29 3rlf 3rum 3ser 3ses 3set 3seu 3sev 3sew 3sex 3sey 3vfj 3w15 3wai 3woa 4b3n 4bl8 4bl9 4bla 4blb 4bld 4dxb 4dxc 4edq 4egc 4exk 4fe8 4feb 4fec 4fed 4giz 4gli 4ifp 4ikm 4irl 4jbz 4jkm 4keg 4khz 4ki0 4kv3 4kyc 4kyd 4kye 4log 4mbp 4n4x 4ndz 4o2x 4ogm 4pe2 4qsz 4qvh 4r0y 4rg5 4rwf 4rwg 4tsm 4wjv 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4wrn 4wth 4wvh 4xa2 4xhs 4xr8 4xzs 4xzv 5aq9 5az6 5az7 5az8 5az9 5aza 5b3w 5b3x 5b3y 5b3z 5c7r 5cbn 5cfv 5dfm 5dis 5e24 5edu 5fio 5fsg 5gru 5gs2 5h7n 5h7q 5hz7 5hzv 5hzw 5i04 5i69 5ihj 5ii5 5iic 5iqz 5jj4 5jst 5jtq 5jtr 5ldf 5t03 5t05 5t0a 5ttd 5wpz 5wq6
        NEDD8_HUMAN | Q158431ndd 1r4m 1r4n 1xt9 2bkr 2ko3 2n7k 3dbh 3dbl 3dbr 3dqv 3gzn 4f8c 4fbj 4hcp 4p5o
        UBA3_HUMAN | Q8TBC41r4m 1r4n 1tt5 1y8x 1yov 2lq7 3dbh 3dbl 3dbr 3fn1 3gzn 5jjm
        UBC12_HUMAN | P610811tt5 1y8x 3tdu 3tdz 4gao 4p5o
        ULA1_HUMAN | Q135641r4m 1r4n 1tt5 1yov 3dbh 3dbl 3dbr 3gzn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2NVU)