5GAR

Thermus thermophilus V/A-ATPase, conformation 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 113: 3245-3250

  • DOI: 10.1073/pnas.1521990113
  • Primary Citation of Related Structures:  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 th ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase alpha chain
A, B, C
577Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: atpA
EC: 3.6.3.14
Find proteins for Q56403 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56403
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase beta chain
D, E, F
457Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: atpB
Find proteins for Q56404 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56404
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase subunit E
G, H
186Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: atpE (vatE)
Find proteins for P74901 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P74901
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-type ATPase subunit G
I, J
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)N/A
Find proteins for Q5SIT5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIT5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase subunit D
K
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: atpD (vatD)
Find proteins for O87880 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  O87880
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase subunit F
L
100Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: atpF (vatF)
Find proteins for P74903 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P74903
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase subunit C
M
323Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: atpC
Find proteins for P74902 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P74902
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Archaeal/vacuolar-type H+-ATPase subunit I
N
652Thermus thermophilus JL-18N/A
Find proteins for H9ZQR4 (Thermus thermophilus JL-18)
Go to UniProtKB:  H9ZQR4
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Vacuolar type ATP synthase subunit
O, P, Q, R, S, T, U, V, W, X, Y, Z
99Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)N/A
Find proteins for Q5SIT7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIT7
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Canadian Institutes of Health ResearchCanadaMOP 81294

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2016-05-25
    Type: Database references