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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HETEROTRIMERIC EGCHEAD PERIPHERAL STALK COMPLEX OF THE YEAST VACUOLAR ATPASE - SECOND CONFORMATION
 
Authors :  R. A. Oot, L. S. Huang, E. A. Berry, S. Wilkens
Date :  29 Mar 12  (Deposition) - 10 Oct 12  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym./Biol. Unit :  C,E,G
Keywords :  Heterotrimer, Peripheral Stalk, Vacuolar Atpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Oot, L. S. Huang, E. A. Berry, S. Wilkens
Crystal Structure Of The Yeast Vacuolar Atpase Heterotrimeric Egc(Head) Peripheral Stalk Complex.
Structure V. 20 1881 2012
PubMed-ID: 23000382  |  Reference-DOI: 10.1016/J.STR.2012.08.020

(-) Compounds

Molecule 1 - V-TYPE PROTON ATPASE SUBUNIT C
    Chains: C
    EC Number: 3.6.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMALC2E
    Expression System Strain: ROSETTA2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 158-277
    Gene: VAT3, VATC, VMA5, YKL080W, YKL410
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: V-ATPASE SUBUNIT C, V-ATPASE 42 KDA SUBUNIT, VACUOLAR PROTON PUMP SUBUNIT C
 
Molecule 2 - V-TYPE PROTON ATPASE SUBUNIT G
    Chains: G
    EC Number: 3.6.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMALC2E
    Expression System Strain: ROSETTA2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VMA10, YHR039BC, YHR039C-A, YHR039C-B
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: V-ATPASE SUBUNIT G, V-ATPASE 13 KDA SUBUNIT, VACUOLAR PROTON PUMP SUBUNIT G
 
Molecule 3 - V-TYPE PROTON ATPASE SUBUNIT E
    Chains: E
    EC Number: 3.6.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMALC2E
    Expression System Strain: ROSETTA2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: O6241, VAT5, VMA4, YOR332W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: V-ATPASE SUBUNIT E, V-ATPASE 27 KDA SUBUNIT, VACUOLAR PROTON PUMP SUBUNIT E

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : CEG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU C:175 , ARG C:258 , GLU C:259BINDING SITE FOR RESIDUE SO4 C 301
2AC2SOFTWAREARG G:25BINDING SITE FOR RESIDUE SO4 G 201
3AC3SOFTWARELYS E:31 , ARG G:25 , ARG G:28BINDING SITE FOR RESIDUE SO4 G 202
4AC4SOFTWAREHIS G:18 , SER G:22 , ARG G:25BINDING SITE FOR RESIDUE SO4 G 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EFA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EFA)

(-) 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 C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhh......eeeeeeeee..hhhhhhhhhhhh.........eeeee...eeeeeeeee..hhhhhhhhhhhh..eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4efa C 158 NLAAAERKKTGDLSVRSLHDIVKPEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFKKNVQEFTTAAREKKFIPREFNYS 263
                                   167       177       187       197       207       217       227       237       247       257      


Chain E from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhh.hhhhhhhhhhhhh......eeee............eeeee......eeeeehhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4efa E   2 SSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPS 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     


Chain G from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4efa G   2 SQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKP 105
                                    11        21        31        41        51        61|       80        90       100     
                                                                                      61|                                  
                                                                                       71
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  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 4EFA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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  4efa
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  VATE_YEAST | P22203
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  VATG_YEAST | P48836
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  3.6.3.14
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 Related Entries

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

UniProtKB/Swiss-Prot
        VATC_YEAST | P31412: 1u7l 3j9t 3j9u 3j9v 4dl0 5vox 5voy 5voz
        VATE_YEAST | P22203: 2kz9 3j9t 3j9u 3j9v 4dl0 5bw9 5d80 5vox 5voy 5voz
        VATG_YEAST | P48836: 2k88 2kwy 3j9t 3j9u 3j9v 4dl0 5bw9 5d80 5vox 5voy 5voz

(-) Related Entries Specified in the PDB File

4dl0 SAME PROTEIN COMPLEX, DIFFERENT CONFORMATION