7TMT

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


This is version 1.4 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 of 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.


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
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar proton pump subunit B
B, D, F
517Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-ATPase subunit E
G, I, K
233Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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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
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit D256Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit F118Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit C392Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit H478Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
V0 assembly protein 1R [auth b]265Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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
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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
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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
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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
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit c160Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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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
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UniProt GroupP32842
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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 

Structure Validation

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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