5GAR

Thermus thermophilus V/A-ATPase, conformation 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.40 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

Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance.

Schep, D.G.Zhao, J.Rubinstein, J.L.

(2016) Proc Natl Acad Sci U S A 113: 3245-3250

  • DOI: https://doi.org/10.1073/pnas.1521990113
  • Primary Citation of Related Structures:  
    5GAR, 5GAS, 5I1M

  • PubMed Abstract: 

    Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases.


  • Organizational Affiliation

    The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G0A4; Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada M5G1L7;


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase alpha chain
A, B, C
577Thermus thermophilusMutation(s): 0 
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for Q56403 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ56403
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase beta chain
D, E, F
457Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q56404 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit E
G, H
186Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P74901 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATPase subunit G
I, J
105Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SIT5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit D210Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for O87880 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit F100Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit C323Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Archaeal/vacuolar-type H+-ATPase subunit I652Thermus thermophilusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for H9ZQR4 (Thermus thermophilus JL-18)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar type ATP synthase subunit
O, P, Q, R, S
O, P, Q, R, S, T, U, V, W, X, Y, Z
99Thermus thermophilusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5SIT7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP 81294

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2016-05-25
    Changes: Database references
  • Version 1.3: 2020-01-15
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references