5TJ5

Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.

Mazhab-Jafari, M.T.Rohou, A.Schmidt, C.Bueler, S.A.Benlekbir, S.Robinson, C.V.Rubinstein, J.L.

(2016) Nature 539: 118-122

  • DOI: 10.1038/nature19828
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V 1 ...

    Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V 1 region drives proton translocation through the membrane-embedded V O region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V 1 and V O regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the V O complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits ac 8 c'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit aA680Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPH1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
membrane-embedded VO motor of V-ATPase
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32563
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c''B213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA16PPA1YHR026W
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
membrane-embedded VO motor of V-ATPase
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P23968
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit c'D147Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA11CLS9TFP3YPL234CP1064
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
membrane-embedded VO motor of V-ATPase
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32842
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit cE, F, G, H, I, J, M, N150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA3CLS7CUP5GEF2YEL027W
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
membrane-embedded VO motor of V-ATPase
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit eL57Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA9CWH36LDB10YCL005W-A
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
membrane-embedded VO motor of V-ATPase
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit fO54Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type proton ATPase subunit dP297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA6
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Vacuolar ATPase (V-ATPase)
Protein: 
membrane-embedded VO motor of V-ATPase
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32366 
Go to UniProtKB:  P32366
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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)CanadaMOP81294
Wellcome TrustUnited KingdomWT008150
Wellcome TrustUnited KingdomWT099141
European Research Council (ERC)European UnionERC268851

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2016-11-16
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-03-28
    Changes: Data collection, Derived calculations
  • Version 1.5: 2020-01-15
    Changes: Author supporting evidence