3J9T

Yeast V-ATPase state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history


Literature

Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase.

Zhao, J.Benlekbir, S.Rubinstein, J.L.

(2015) Nature 521: 241-245

  • DOI: https://doi.org/10.1038/nature14365
  • Primary Citation of Related Structures:  
    3J9T, 3J9U, 3J9V

  • PubMed Abstract: 

    Eukaryotic vacuolar H(+)-ATPases (V-ATPases) are rotary enzymes that use energy from hydrolysis of ATP to ADP to pump protons across membranes and control the pH of many intracellular compartments. ATP hydrolysis in the soluble catalytic region of the enzyme is coupled to proton translocation through the membrane-bound region by rotation of a central rotor subcomplex, with peripheral stalks preventing the entire membrane-bound region from turning with the rotor. The eukaryotic V-ATPase is the most complex rotary ATPase: it has three peripheral stalks, a hetero-oligomeric proton-conducting proteolipid ring, several subunits not found in other rotary ATPases, and is regulated by reversible dissociation of its catalytic and proton-conducting regions. Studies of ATP synthases, V-ATPases, and bacterial/archaeal V/A-ATPases have suggested that flexibility is necessary for the catalytic mechanism of rotary ATPases, but the structures of different rotational states have never been observed experimentally. Here we use electron cryomicroscopy to obtain structures for three rotational states of the V-ATPase from the yeast Saccharomyces cerevisiae. The resulting series of structures shows ten proteolipid subunits in the c-ring, setting the ATP:H(+) ratio for proton pumping by the V-ATPase at 3:10, and reveals long and highly tilted transmembrane α-helices in the a-subunit that interact with the c-ring. The three different maps reveal the conformational changes that occur to couple rotation in the symmetry-mismatched soluble catalytic region to the membrane-bound proton-translocating region. Almost all of the subunits of the enzyme undergo conformational changes during the transitions between these three rotational states. The structures of these states provide direct evidence that deformation during rotation enables the smooth transmission of power through rotary ATPases.


  • Organizational Affiliation

    1] Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada [2] Department of Medical Biophysics, The University of Toronto, Toronto Medical Discovery Tower, MaRS Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit DA [auth M]256Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP32610
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit FB [auth N]118Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P39111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP39111
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase catalytic subunit AC [auth A],
E [auth C],
G [auth E]
616Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14 (PDB Primary Data), 3.1 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P17255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP17255
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit BD [auth B],
F [auth D],
H [auth F]
517Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P16140 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit dI [auth Q]345Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32366
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit GJ [auth L],
O [auth H],
Q [auth J]
114Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit EK,
P [auth G],
R [auth I]
233Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit HL [auth P]478Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformM [auth b]840Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
V-type proton ATPase subunit CN [auth O]392Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
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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UniProt GroupP25515
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Refinement description