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(-) Description

Title :  THE IDOL-UBE2D COMPLEX MEDIATES STEROL-DEPENDENT DEGRADATION OF THE LDL RECEPTOR
 
Authors :  L. Fairall, B. T. Goult, C. J. Millard, P. Tontonoz, J. W. R. Schwabe
Date :  04 May 11  (Deposition) - 29 Jun 11  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Ligase, E2 Ligase-E3 Ligase Complex, Ring Zinc-Finger, Ubl Conjugation Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Zhang, L. Fairall, B. T. Goult, A. C. Calkin, C. Hong, C. J. Millard, P. Tontonoz, J. W. Schwabe
The Idol-Ube2D Complex Mediates Sterol-Dependent Degradation Of The Ldl Receptor.
Genes Dev. V. 25 1262 2011
PubMed-ID: 21685362  |  Reference-DOI: 10.1101/GAD.2056211

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE MYLIP
    ChainsA, C, E, G
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRING, RESIDUES 369-445
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymINDUCIBLE DEGRADER OF THE LDL-RECEPTOR, IDOL, MYOSIN REGULATORY LIGHT CHAIN INTERACTING PROTEIN, MIR
 
Molecule 2 - UBIQUITIN-CONJUGATING ENZYME E2 D1
    ChainsB, D, F, H
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSTIMULATOR OF FE TRANSPORT, SFT, UBC4/5 HOMOLOG, UBCH5, UBIQUITIN CARRIER PROTEIN D1, UBIQUITIN-CONJUGATING ENZYME E2(17)KB 1, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 1, UBIQUITIN-PROTEIN LIGASE D1, UBE2D1

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB      
Biological Unit 2 (1x)  CD    
Biological Unit 3 (1x)    EF  
Biological Unit 4 (1x)      GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1ACT9Ligand/IonACETATE ION
2ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:387 , CYS A:390 , CYS A:408 , CYS A:411BINDING SITE FOR RESIDUE ZN A1001
02AC2SOFTWARECYS A:402 , HIS A:404 , CYS A:418 , CYS A:421BINDING SITE FOR RESIDUE ZN A1002
03AC3SOFTWARECYS C:387 , CYS C:390 , CYS C:408 , CYS C:411 , GLY F:-1BINDING SITE FOR RESIDUE ZN C1001
04AC4SOFTWARECYS C:402 , HIS C:404 , CYS C:418 , CYS C:421BINDING SITE FOR RESIDUE ZN C1002
05AC5SOFTWARECYS E:387 , CYS E:390 , CYS E:408 , CYS E:411BINDING SITE FOR RESIDUE ZN E1001
06AC6SOFTWARECYS E:402 , HIS E:404 , CYS E:418 , CYS E:421BINDING SITE FOR RESIDUE ZN E1002
07AC7SOFTWARECYS G:387 , CYS G:390 , CYS G:408 , CYS G:411BINDING SITE FOR RESIDUE ZN G1001
08AC8SOFTWARECYS G:402 , HIS G:404 , CYS G:418 , CYS G:421BINDING SITE FOR RESIDUE ZN G1002
09AC9SOFTWAREILE H:67 , ILE H:84 , HOH H:2034BINDING SITE FOR RESIDUE ACT H1148
10BC1SOFTWAREGLU G:383 , ALA G:384 , LEU G:386 , MET G:388 , HOH G:2024BINDING SITE FOR RESIDUE ACT G1442
11BC2SOFTWAREARG H:5 , LYS H:8BINDING SITE FOR RESIDUE ACT H1149
12BC3SOFTWAREILE B:67 , ILE B:84 , HOH B:2041BINDING SITE FOR RESIDUE ACT B1148
13BC4SOFTWAREILE F:67 , SER F:83 , ILE F:84BINDING SITE FOR RESIDUE ACT F1148
14BC5SOFTWAREPHE B:69 , THR B:70 , SER B:80 , GLY B:82 , HOH B:2043BINDING SITE FOR RESIDUE ACT B1149
15BC6SOFTWAREGLU A:383 , ALA A:384 , LEU A:386 , HOH A:2010BINDING SITE FOR RESIDUE ACT A1439
16BC7SOFTWARESER D:105 , SER D:108 , PRO H:57 , THR H:58BINDING SITE FOR RESIDUE ACT H1150
17BC8SOFTWAREHIS A:404BINDING SITE FOR RESIDUE ACT A1440

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Cys A:400 -Pro A:401
2Tyr B:60 -Pro B:61
3Cys C:400 -Pro C:401
4Tyr D:60 -Pro D:61
5Cys E:400 -Pro E:401
6Tyr F:60 -Pro F:61
7Cys G:400 -Pro G:401
8Tyr H:60 -Pro H:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YHO)

(-) PROSITE Motifs  (3, 12)

Asymmetric Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2D1_HUMAN4-136
 
 
 
  4B:4-136
D:4-136
F:4-136
H:4-136
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2D1_HUMAN74-89
 
 
 
  4B:74-89
D:74-89
F:74-89
H:74-89
3ZF_RING_2PS50089 Zinc finger RING-type profile.MYLIP_HUMAN387-422
 
 
 
  4A:387-422
C:387-422
E:387-422
G:387-422
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2D1_HUMAN4-136
 
 
 
  1B:4-136
-
-
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2D1_HUMAN74-89
 
 
 
  1B:74-89
-
-
-
3ZF_RING_2PS50089 Zinc finger RING-type profile.MYLIP_HUMAN387-422
 
 
 
  1A:387-422
-
-
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2D1_HUMAN4-136
 
 
 
  1-
D:4-136
-
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2D1_HUMAN74-89
 
 
 
  1-
D:74-89
-
-
3ZF_RING_2PS50089 Zinc finger RING-type profile.MYLIP_HUMAN387-422
 
 
 
  1-
C:387-422
-
-
Biological Unit 3 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2D1_HUMAN4-136
 
 
 
  1-
-
F:4-136
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2D1_HUMAN74-89
 
 
 
  1-
-
F:74-89
-
3ZF_RING_2PS50089 Zinc finger RING-type profile.MYLIP_HUMAN387-422
 
 
 
  1-
-
E:387-422
-
Biological Unit 4 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2D1_HUMAN4-136
 
 
 
  1-
-
-
H:4-136
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2D1_HUMAN74-89
 
 
 
  1-
-
-
H:74-89
3ZF_RING_2PS50089 Zinc finger RING-type profile.MYLIP_HUMAN387-422
 
 
 
  1-
-
-
G:387-422

(-) Exons   (7, 28)

Asymmetric Unit (7, 28)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003739101ENSE00001334393chr10:60094735-60094985251UB2D1_HUMAN1-884B:1-8
D:1-8
F:1-8
H:1-8
8
8
8
8
1.2ENST000003739102ENSE00000833888chr10:60121098-6012116164UB2D1_HUMAN9-30224B:9-30
D:9-30
F:9-30
H:9-30
22
22
22
22
1.3ENST000003739103ENSE00000705064chr10:60121255-6012128632UB2D1_HUMAN30-40114B:30-40
D:30-40
F:30-40
H:30-40
11
11
11
11
1.4ENST000003739104ENSE00000705068chr10:60123369-6012344678UB2D1_HUMAN41-66264B:41-66
D:41-66
F:41-66
H:41-66
26
26
26
26
1.5bENST000003739105bENSE00000705083chr10:60124531-60124636106UB2D1_HUMAN67-102364B:67-102
D:67-102
F:67-102
H:67-102
36
36
36
36
1.6ENST000003739106ENSE00001659237chr10:60127683-6012777694UB2D1_HUMAN102-133324B:102-133
D:102-133
F:102-133
H:102-133
32
32
32
32
1.7bENST000003739107bENSE00001334391chr10:60128480-60129403924UB2D1_HUMAN133-147154B:133-147
D:133-147
F:133-147
H:133-147
15
15
15
15

(-) Sequences/Alignments

Asymmetric 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:67
 aligned with MYLIP_HUMAN | Q8WY64 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:67
                                   381       391       401       411       421       431       
          MYLIP_HUMAN   372 RVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTS 438
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...........eeee.......hhhhhh.............eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------ZF_RING_2  PDB: A:387-422           ---------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2yho A 372 RVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTS 438
                                   381       391       401       411       421       431       

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with UB2D1_HUMAN | P51668 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:149
                              1                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138         
          UB2D1_HUMAN     - --MALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
               SCOP domains d2yhob_ B: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----UBIQUITIN_CONJUGAT_2  PDB: B:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) --Exon 1.1Exon 1.2  PDB: B:9-30 ----------Exon 1.4  PDB: B:41-66    Exon 1.5b  PDB: B:67-102            ------------------------------Exon 1.7b       Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3   -------------------------------------------------------------Exon 1.6  PDB: B:102-133        -------------- Transcript 1 (2)
                 2yho B  -1 GAMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138         

Chain C from PDB  Type:PROTEIN  Length:67
 aligned with MYLIP_HUMAN | Q8WY64 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:67
                                   381       391       401       411       421       431       
          MYLIP_HUMAN   372 RVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTS 438
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...........eeee.......hhhhhh.............eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------ZF_RING_2  PDB: C:387-422           ---------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 2yho C 372 RVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTS 438
                                   381       391       401       411       421       431       

Chain D from PDB  Type:PROTEIN  Length:149
 aligned with UB2D1_HUMAN | P51668 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:149
                              1                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138         
          UB2D1_HUMAN     - --MALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
               SCOP domains d2yhod_ D: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----UBIQUITIN_CONJUGAT_2  PDB: D:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) --Exon 1.1Exon 1.2  PDB: D:9-30 ----------Exon 1.4  PDB: D:41-66    Exon 1.5b  PDB: D:67-102            ------------------------------Exon 1.7b       Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3   -------------------------------------------------------------Exon 1.6  PDB: D:102-133        -------------- Transcript 1 (2)
                 2yho D  -1 GAMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138         

Chain E from PDB  Type:PROTEIN  Length:70
 aligned with MYLIP_HUMAN | Q8WY64 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:70
                                   381       391       401       411       421       431       441
          MYLIP_HUMAN   372 RVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTSLLN 441
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...........eeee.......hhhhhh.............eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------ZF_RING_2  PDB: E:387-422           ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2yho E 372 RVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTSLLN 441
                                   381       391       401       411       421       431       441

Chain F from PDB  Type:PROTEIN  Length:149
 aligned with UB2D1_HUMAN | P51668 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:149
                              1                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138         
          UB2D1_HUMAN     - --MALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
               SCOP domains d2yhof_ F: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----UBIQUITIN_CONJUGAT_2  PDB: F:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) --Exon 1.1Exon 1.2  PDB: F:9-30 ----------Exon 1.4  PDB: F:41-66    Exon 1.5b  PDB: F:67-102            ------------------------------Exon 1.7b       Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3   -------------------------------------------------------------Exon 1.6  PDB: F:102-133        -------------- Transcript 1 (2)
                 2yho F  -1 GAMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138         

Chain G from PDB  Type:PROTEIN  Length:70
 aligned with MYLIP_HUMAN | Q8WY64 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:70
                                   381       391       401       411       421       431       441
          MYLIP_HUMAN   372 RVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTSLLN 441
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------zf-C3HC4_3-2yhoG01 G:383-428                  ------------- Pfam domains (1)
           Pfam domains (2) -----------zf-C3HC4_3-2yhoG02 G:383-428                  ------------- Pfam domains (2)
           Pfam domains (3) -----------zf-C3HC4_3-2yhoG03 G:383-428                  ------------- Pfam domains (3)
           Pfam domains (4) -----------zf-C3HC4_3-2yhoG04 G:383-428                  ------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhh...........eeee.......hhhhhhh............eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------ZF_RING_2  PDB: G:387-422           ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2yho G 372 RVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEHVQHVYLPTHTSLLN 441
                                   381       391       401       411       421       431       441

Chain H from PDB  Type:PROTEIN  Length:147
 aligned with UB2D1_HUMAN | P51668 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          UB2D1_HUMAN     1 MALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
               SCOP domains d2yhoh_ H: automated matches                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----UQ_con-2yhoH01 H:5-142                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) ----UQ_con-2yhoH02 H:5-142                                                                                                                    ----- Pfam domains (2)
           Pfam domains (3) ----UQ_con-2yhoH03 H:5-142                                                                                                                    ----- Pfam domains (3)
           Pfam domains (4) ----UQ_con-2yhoH04 H:5-142                                                                                                                    ----- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---UBIQUITIN_CONJUGAT_2  PDB: H:4-136 UniProt: 4-136                                                                                    ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1Exon 1.2  PDB: H:9-30 ----------Exon 1.4  PDB: H:41-66    Exon 1.5b  PDB: H:67-102            ------------------------------Exon 1.7b       Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.3   -------------------------------------------------------------Exon 1.6  PDB: H:102-133        -------------- Transcript 1 (2)
                 2yho H   1 MALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YHO)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: RING (39)
(-)
Clan: UBC (69)

(-) Gene Ontology  (46, 53)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G   (MYLIP_HUMAN | Q8WY64)
molecular function
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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: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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0010989    negative regulation of low-density lipoprotein particle clearance    Any process that decreases the rate, frequency or extent of low-density lipoprotein particle clearance. Low-density lipoprotein particle clearance is the process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0031648    protein destabilization    Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0032803    regulation of low-density lipoprotein particle receptor catabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of low-density lipoprotein particle receptors.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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,D,F,H   (UB2D1_HUMAN | P51668)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0061631    ubiquitin conjugating enzyme activity    Isoenergetic transfer of ubiquitin from one protein to another via the reaction X-ubiquitin + Y -> Y-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    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:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0035666    TRIF-dependent toll-like receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
    GO:0031145    anaphase-promoting complex-dependent 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 ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0051436    negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
    GO:0031398    positive regulation of protein ubiquitination    Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0051437    positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition    Any process that activates, maintains or increases the rate of ubiquitin ligase activity that contributes to the regulation of the mitotic cell cycle phase transition.
    GO:0043161    proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
    GO:0070936    protein K48-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0051439    regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    A cell cycle process that modulates the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    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: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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MYLIP_HUMAN | Q8WY642yhn
        UB2D1_HUMAN | P516682c4p 3oj4 3ptf 4ap4 4qpl 5fer

(-) Related Entries Specified in the PDB File

2c4p CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-CONJUGATING ENZYME UBCH5A
2yhn THE IDOL-UBE2D COMPLEX MEDIATES STEROL-DEPENDENT DEGRADATION OF THE LDL RECEPTOR