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(-) Description

Title :  QUANTITATIVE INTERACTION MAPPING REVEALS AN EXTENDED UBIQUITIN REGULATORY DOMAIN IN ASPL THAT DISRUPTS FUNCTIONAL P97 HEXAMERS AND INDUCES CELL DEATH
 
Authors :  Y. Roske, A. Arumughan, U. Heinemann, E. Wanker
Date :  26 Feb 16  (Deposition) - 26 Oct 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aspl, P97, Disassembly, Eubx, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Arumughan, Y. Roske, C. Barth, L. L. Forero, K. Bravo-Rodriguez, A. Redel, S. Kostova, E. Mcshane, R. Opitz, K. Faelber, K. Rau, T. Mielke, O. Daumke, M. Selbach, E. Sanchez-Garcia, O. Rocks, D. Panakova, U. Heinemann, E. E. Wanker
Quantitative Interaction Mapping Reveals An Extended Ubx Domain In Aspl That Disrupts Functional P97 Hexamers.
Nat Commun V. 7 13047 2016
PubMed-ID: 27762274  |  Reference-DOI: 10.1038/NCOMMS13047

(-) Compounds

Molecule 1 - TETHER CONTAINING UBX DOMAIN FOR GLUT4
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQLINKG
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 317-553
    Gene: ASPSCR1, ASPL, RCC17, TUG, UBXD9, UBXN9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALVEOLAR SOFT PART SARCOMA CHROMOSOMAL REGION CANDIDATE GENE 1 PROTEIN,ALVEOLAR SOFT PART SARCOMA LOCUS,RENAL PAPILLARY CELL CARCINOMA PROTEIN 17,UBX DOMAIN-CONTAINING PROTEIN 9
 
Molecule 2 - TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE
    Chains: B, D
    EC Number: 3.6.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQLINKG
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector Type: PLASMID
    Gene: VCP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TER ATPASE,15S MG(2+)-ATPASE P97 SUBUNIT,VALOSIN-CONTAINING PROTEIN,VCP

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:205 , GLY B:207 , GLY B:248 , THR B:249 , GLY B:250 , LYS B:251 , THR B:252 , LEU B:253 , ILE B:380 , HIS B:384 , GLY B:408 , ALA B:409 , MG B:502 , HOH B:656 , HOH B:661binding site for residue ADP B 501
2AC2SOFTWAREADP B:501binding site for residue MG B 502
3AC3SOFTWAREARG B:359 , ARG B:362 , HOH B:699binding site for residue SO4 B 503
4AC4SOFTWAREARG B:147 , LYS B:148binding site for residue EDO B 504
5AC5SOFTWAREASN B:36 , LEU B:153 , VAL B:154 , ARG B:155 , HOH B:660 , HOH B:723binding site for residue EDO B 505
6AC6SOFTWARETHR B:180 , ILE B:182 , HOH B:685binding site for residue GOL B 506
7AC7SOFTWAREASP D:205 , GLY D:207 , GLY D:248 , THR D:249 , GLY D:250 , LYS D:251 , THR D:252 , LEU D:253 , ILE D:380 , HIS D:384 , GLY D:408 , ALA D:409 , MG D:502 , HOH D:629binding site for residue ADP D 501
8AC8SOFTWAREADP D:501binding site for residue MG D 502
9AC9SOFTWAREGLN D:398 , HOH D:616binding site for residue EDO D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IFS)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Thr A:436 -Pro A:437
2Pro A:437 -Pro A:438
3Phe A:455 -Pro A:456
4Asp B:169 -Pro B:170
5Ser B:171 -Pro B:172
6Ala B:297 -Pro B:298
7Thr C:436 -Pro C:437
8Pro C:437 -Pro C:438
9Phe C:455 -Pro C:456
10Asp D:169 -Pro D:170
11Ser D:171 -Pro D:172
12Ala D:297 -Pro D:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IFS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IFS)

(-) Exons   (0, 0)

(no "Exon" information available for 5IFS)

(-) 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:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeehhhhh..........hhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..eeeeee.....eeeeee....hhhhhhhhhhhh........eeee....ee...............eeeeeee.........hhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ifs A 317 PVDREPVVCHPDLEERLQAWPAELPDEFFELTVDDVRRRLAQLKSERKRLEEAPLVTKAFREAQIKEKLERYPKVALRVLFPDRYVLQGFFRPSETVGDLRDFVRSHLGNPELSFYLFITPPKTVLDDHTQTLFQANLFPAALVHLGAEEPAGVYLEPGLLEHAISPSAADVLVARYMSRA 497
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496 


Chain B from PDB  Type:PROTEIN  Length:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.......eeeehhhhhhhhh.....eeeee.....eeeeeeee.......eeeehhhhhhhh......eeeeee........eeeeeehhhhhh.ee.hhhhhhhhhhhh....eee...eeeeee..eeeeeeeeeee...eee.....eee..................hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.eeeeeehhhhhh...hhhhhhhhhhhhhhhhh..eeeeeehhhhh............hhhhhhhhhhhhh.hhhh.eeeeeee.hhhhhhhhhhh.....eeee....hhhhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eehhhhhh...hhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ifs B  21 NRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMEDETIDAEVMNSLAVTMDDFRWALSQSNPQVTWEDIG 480
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420      |435       445       455     ||476    
                                                                                                                                                                                                                                                                                                                                                                                                                                                427|                         461|       
                                                                                                                                                                                                                                                                                                                                                                                                                                                 433                          473       


Chain C from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeehhhhh..........hhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..eeeeee.....eeeeee....hhhhhhhhhhh.........eeee....ee...............eeeeeee.....hhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ifs C 318 VDREPVVCHPDLEERLQAWPAELPDEFFELTVDDVRRRLAQLKSERKRLEEAPLVTKAFREAQIKEKLERYPKVALRVLFPDRYVLQGFFRPSETVGDLRDFVRSHLGNPELSFYLFITPPKTVLDDHTQTLFQANLFPAALVHLGAEEYLEPGLLEHAISPSAADVLVARYMS 495
                                   327       337       347       357       367       377       387       397       407       417       427       437       447       457       471       481       491    
                                                                                                                                                                              466|                        
                                                                                                                                                                               471                        


Chain D from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee........eeeehhhhhhhh.....eeeeee.....eeeeeeee.......eee.hhhhhhhh......eeeeee........eeeeee.hhhh..ee.hhhhhhhhhhhh...eeee...eeeeee..eeeeeeeeeee...eeee....eee..................hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhh.eeeeeehhhhh..hhhhhhhhhhhhhhhhh..eeeeeehhhhh............hhhhhhhhhhhhh.hhhh.eeeeeee.hhhhh...........eeee....hhhhhhhhhhhhh...ee....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....eehhhhhh.eehhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ifs D  21 NRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMLEDETIDAEVMNSLAVTMDDFRWALSQSNPQVTWEDIG 480
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     ||282       292       302       312       322       332       342       352       362       372       382       392       402       412       422    || 436       446       456    || 477   
                                                                                                                                                                                                                                                                                         276|                                                                                                                                                 427|                          461|       
                                                                                                                                                                                                                                                                                          279                                                                                                                                                  432                           473
   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  (0, 0)

(no "SCOP Domain" information available for 5IFS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IFS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IFS)

(-) Gene Ontology  (85, 92)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:297 - Pro B:298   [ RasMol ]  
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 Related Entries

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        ASPC1_HUMAN | Q9BZE9: 5ifw
        TERA_HUMAN | P55072: 3ebb 3hu1 3hu2 3hu3 3qc8 3qq7 3qq8 3qwz 3tiw 4kdi 4kdl 4kln 4ko8 4kod 4p0a 5b6c 5c18 5c19 5c1a 5c1b 5dyg 5dyi 5epp 5ftj 5ftk 5ftl 5ftm 5ftn 5glf 5ifw 5x4l

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