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(-) Description

Title :  METALLOSPHERA SEDULA VPS4 CRYSTAL STRUCTURE
 
Authors :  C. Caillat, P. Macheboeuf, Y. Wu, A. A. Mccarthy, E. Boeri-Erba, G. Effa H. G. Gottlinger, W. Weissenhorn, P. Renesto
Date :  02 Dec 14  (Deposition) - 28 Oct 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hydrolase, Atpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Caillat, P. Macheboeuf, Y. Wu, A. A. Mccarthy, E. Boeri-Erba, G. Effantin, H. G. Gottlinger, W. Weissenhorn, P. Renesto
Asymmetric Ring Structure Of Vps4 Required For Escrt-Iii Disassembly.
Nat. Commun. V. 6 8781 2015
PubMed-ID: 26632262  |  Reference-DOI: 10.1038/NCOMMS9781

(-) Compounds

Molecule 1 - AAA ATPASE, CENTRAL DOMAIN PROTEIN
    Chains: A, B, C, D, E, F
    EC Number: 3.6.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST-17
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C41
    Expression System Vector Type: PLASMID
    Fragment: AAA, UNP RESIDUES 75-369
    Organism Scientific: METALLOSPHAERA SEDULA
    Organism Taxid: 43687
    Other Details: TRUNCATION OF THE NTERMINUS 74 RESIDUES
    Synonym: VPS4

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4D80)

(-) Sites  (0, 0)

(no "Site" information available for 4D80)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D80)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:333 -Ala A:334
2Lys A:365 -Phe A:366
3Asn B:100 -Glu B:101
4Asn E:100 -Glu E:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D80)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D80)

(-) Exons   (0, 0)

(no "Exon" information available for 4D80)

(-) 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:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhh.........hhhhhhhhhhhhhhh........eeeeee......hhhhhh...eeee....hhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d80 A  97 VTLNEIVGLEDVKEALKEAVVYPSKRPDLFPLGWPRGILLYGPPGCGKTMIAAAVANELDSEFIHVDAASIMSKAEKNVAKIFKTARELSKKENKPAIIFIDELDALLASYTSEVGGEARVRNQFLKEMDGLADKNEISKVYVIGATNKPWRLDEPFLRRFQKRIYITLPDKAHRLELLKHYSSKVKLDPNVNLEELAELTDGYTASDIRDIVQSAHMRVVKEMFEKNLQEPRAINMDDFREVLKVRKPSVNQDMLKAYAAWHEKFKAL 369
                                   106       116       126       136       146       156       166   ||  180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360         
                                                                                                   170|                                                                                                                                                                                                  
                                                                                                    175                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhhh.......eeeeehhhhhh.....hhhhhhhhhhhhhhh....eeeeee......hhhhhh...eeee....hhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d80 B  98 TLNEIVGLEDVKEALKEAVVYPSKRPDLFPLGWPRGILLYGPPGCGKTMIAAAVANELDSEFIHVDAASIMGEAEKNVAKIFKTARELSKKENKPAIIFIDELDALLEVGGEARVRNQFLKEMDGLAISKVYVIGATNKPWRLDEPFLRRFQKRIYITLPDKAHRLELLKHYSSKVKLDPNVNLEELAELTDGYTASDIRDIVQSAHMRVVKEMFEKNLQEPRAINMDDFREVLKVRKPSVNQDMLKAYAAWHEKFK 367
                                   107       117       127       137       147       157       167||     181       191       201      |216       226      |240       250       260       270       280       290       300       310       320       330       340       350       360       
                                                                                                168|                                208|                233|                                                                                                                                 
                                                                                                 173                                 214                 238                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh...eeeeehhhhhhh....hhhhhhhhhhhhhhhh.......eeeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhh........eeeeee......hhhhhh...eeee....hhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d80 C  96 KVTLNEIVGLEDVKEALKEAVVYPSKRPDLFPLGWPRGILLYGPPGCGKTMIAAAVANELDSEFIHVDAASIMSKWLGEAEKNVAKIFKTARELSKKENKPAIIFIDELDALLASYTSEVGGEARVRNQFLKEMDGLADKNEISKVYVIGATNKPWRLDEPFLRRFQKRIYITLPDKAHRLELLKHYSSKVKLDPNVNLEELAELTDGYTASDIRDIVQSAHMRVVKEMFEKNLQEPRAINMDDFREVLKVRKPSVNQDMLKAYAAWHEKFK 367
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  


Chain D from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh...eeeeehhhhhhh....hhhhhhhhhhhhhhhh.......eeeeehhhhhhh.........hhhhhhhhhhhhhhh........eeeeee......hhhhhh...eeee....hhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d80 D  97 VTLNEIVGLEDVKEALKEAVVYPSKRPDLFPLGWPRGILLYGPPGCGKTMIAAAVANELDSEFIHVDAASIMSKWLGEAEKNVAKIFKTARELSKKENKPAIIFIDELDALLASYTSEVGGEARVRNQFLKEMDGLADKNEISKVYVIGATNKPWRLDEPFLRRFQKRIYITLPDKAHRLELLKHYSSKVKLDPNVNLEELAELTDGYTASDIRDIVQSAHMRVVKEMFEKNLQEPRAINMDDFREVLKVRKPSVNQDMLKAYAAWHEKFKAL 369
                                   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   


Chain E from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh...eeeeehhhhh.hhhhhhhhhhhhhhhh.......eeeeehhhhhh.....hhhhhhhhhhhhhhh........eeeeee......hhhhhh...eeee....hhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d80 E  96 KVTLNEIVGLEDVKEALKEAVVYPSKRPDLFPLGWPRGILLYGPPGCGKTMIAAAVANELDSEFIHVDAASIMEAEKNVAKIFKTARELSKKENKPAIIFIDELDALLEVGGEARVRNQFLKEMDGLADKNEISKVYVIGATNKPWRLDEPFLRRFQKRIYITLPDKAHRLELLKHYSSKVKLDPNVNLEELAELTDGYTASDIRDIVQSAHMRVVKEMFEKNLQEPRAINMDDFREVLKVRKPSVNQDMLKAYAAWHEKFK 367
                                   105       115       125       135       145       155       165  ||   180       190       200       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  
                                                                                                  168|                               208|                                                                                                                                                         
                                                                                                   174                                214                                                                                                                                                         


Chain F from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh...eeeeehhhhhhh....hhhhhhhhhhhhhhhh.......eeeeehhhhhhh.........hhhhhhhhhhhhhhh........eeeeee......hhhhhh...eeee....hhhhhhhhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d80 F  96 KVTLNEIVGLEDVKEALKEAVVYPSKRPDLFPLGWPRGILLYGPPGCGKTMIAAAVANELDSEFIHVDAASIMSKWLGEAEKNVAKIFKTARELSKKENKPAIIFIDELDALLASYTSEVGGEARVRNQFLKEMDGLADKNEISKVYVIGATNKPWRLDEPFLRRFQKRIYITLPDKAHRLELLKHYSSKVKLDPNVNLEELAELTDGYTASDIRDIVQSAHMRVVKEMFEKNLQEPRAINMDDFREVLKVRKPSVNQDMLKAYAAWHEKFKAL 369
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365
   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 4D80)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D80)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D80)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:333 - Ala A:334   [ RasMol ]  
    Asn B:100 - Glu B:101   [ RasMol ]  
    Asn E:100 - Glu E:101   [ RasMol ]  
    Lys A:365 - Phe A:366   [ RasMol ]  
 

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 Related Entries

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        A4YHC5_METS5 | A4YHC5: 4d81 4d82

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