7TMT | pdb_00007tmt

V-ATPase from Saccharomyces cerevisiae, State 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Coordinated conformational changes in the V 1 complex during V-ATPase reversible dissociation.

Vasanthakumar, T.Keon, K.A.Bueler, S.A.Jaskolka, M.C.Rubinstein, J.L.

(2022) Nat Struct Mol Biol 29: 430-439

  • DOI: https://doi.org/10.1038/s41594-022-00757-z
  • Primary Citation Related Structures: 
    7TMM, 7TMO, 7TMP, 7TMQ, 7TMR, 7TMS, 7TMT

  • PubMed Abstract: 

    Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V 1 region that hydrolyzes ATP and a membrane-embedded V O region that transports protons. V-ATPase activity is regulated by reversible dissociation of the two regions, with the isolated V 1 and V O complexes becoming autoinhibited on disassembly and subunit C subsequently detaching from V 1 . In yeast, assembly of the V 1 and V O regions is mediated by the regulator of the ATPase of vacuoles and endosomes (RAVE) complex through an unknown mechanism. We used cryogenic-electron microscopy of yeast V-ATPase to determine structures of the intact enzyme, the dissociated but complete V 1 complex and the V 1 complex lacking subunit C. On separation, V 1 undergoes a dramatic conformational rearrangement, with its rotational state becoming incompatible for reassembly with V O . Loss of subunit C allows V 1 to match the rotational state of V O , suggesting how RAVE could reassemble V 1 and V O by recruiting subunit C.


  • Organizational Affiliation
    • Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 989.86 kDa 
  • Atom Count: 53,433 
  • Modeled Residue Count: 8,221 
  • Deposited Residue Count: 8,952 
  • Unique protein chains: 16

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H(+)-transporting two-sector ATPase
A, C, E
617Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for B3LH69 (Saccharomyces cerevisiae (strain RM11-1a))
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UniProt GroupB3LH69
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar proton pump subunit B
B, D, F
517Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
V-ATPase subunit E
G, I, K
233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit G
H, J, L
114Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit D256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit F118Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C392Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit H478Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P41807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformQ [auth a]840Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
V0 assembly protein 1R [auth b]265Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c''S [auth c]213Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit dT [auth d]345Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit eU [auth e]73Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Yeast V-ATPase subunit fV [auth f]85Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c160Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c'EA [auth o]164Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
FA [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT166152

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2022-05-11
    Changes: Database references
  • Version 1.3: 2022-06-01
    Changes: Database references
  • Version 1.4: 2024-02-21
    Changes: Data collection
  • Version 1.5: 2025-05-28
    Changes: Data collection, Structure summary