7VAU

V1EG of V/A-ATPase from Thermus thermophilus at low ATP concentration, state2-2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases.

Kishikawa, J.Nakanishi, A.Nakano, A.Saeki, S.Furuta, A.Kato, T.Mistuoka, K.Yokoyama, K.

(2022) Nat Commun 13: 1213-1213

  • DOI: https://doi.org/10.1038/s41467-022-28832-5
  • Primary Citation of Related Structures:  
    7VAI, 7VAJ, 7VAK, 7VAL, 7VAM, 7VAN, 7VAO, 7VAP, 7VAQ, 7VAR, 7VAS, 7VAT, 7VAU, 7VAV, 7VAW, 7VAX, 7VAY, 7VB0

  • PubMed Abstract: 

    V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with F o F 1 ATP synthase. When powered by ATP hydrolysis, the V 1 domain rotates the central rotor against the A 3 B 3 hexamer, composed of three catalytic AB dimers adopting different conformations (AB open , AB semi , and AB closed ). Here, we report the atomic models of 18 catalytic intermediates of the V 1 domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not rotate immediately after binding of ATP to the V 1 . Instead, three events proceed simultaneously with the 120˚ rotation of the shaft: hydrolysis of ATP in AB semi , zipper movement in AB open by the binding ATP, and unzipper movement in AB closed with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in AB semi , rather than the power stroke model proposed previously for F 1 -ATPase.


  • Organizational Affiliation

    Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, Kyoto, 603-8555, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase alpha chain
A, B, C
578Thermus thermophilus HB8Mutation(s): 0 
EC: 7.1.2.2
UniProt
Find proteins for Q56403 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56403 
Go to UniProtKB:  Q56403
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56403
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase beta chain
D, E, F
478Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q56404 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56404 
Go to UniProtKB:  Q56404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56404
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit D223Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for O87880 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore O87880 
Go to UniProtKB:  O87880
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87880
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit F104Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P74903 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P74903 
Go to UniProtKB:  P74903
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74903
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit G
I, K
120Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SIT5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIT5 
Go to UniProtKB:  Q5SIT5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIT5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
V-type ATP synthase subunit E
J, L
188Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P74901 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P74901 
Go to UniProtKB:  P74901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74901
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H03231
Japan Society for the Promotion of Science (JSPS)Japan20K06514
Japan Agency for Medical Research and Development (AMED)JapanJP17am0101001
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan12024046
Japan Society for the Promotion of Science (JSPS)Japan20J00162
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan20215008

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection