6LY8

V/A-ATPase from Thermus thermophilus, the soluble domain, including V1, d, two EG stalks, and N-terminal domain of a-subunit.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Mechanical inhibition of isolated V o from V/A-ATPase for proton conductance.

Kishikawa, J.I.Nakanishi, A.Furuta, A.Kato, T.Namba, K.Tamakoshi, M.Mitsuoka, K.Yokoyama, K.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.56862
  • Primary Citation of Related Structures:  
    6LY8, 6LY9

  • PubMed Abstract: 

    V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V 1 domain, with proton flow through the V o membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V 1 domain, the V o domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the V o domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and isolated V o at near-atomic resolution, respectively. These structures clarify how the isolated V o domain adopts the auto-inhibited form and how the holo complex prevents formation of the inhibited V o form.


  • Organizational Affiliation

    Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.


Macromolecules
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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
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  • Reference Sequence
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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
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UniProt GroupQ56404
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  • Reference Sequence
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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
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UniProt GroupO87880
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  • Reference Sequence
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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  
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UniProt GroupP74903
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
I [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
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)Japan17H03648
Japan Agency for Medical Research and Development (AMED)JapanJP17am0101001
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan12024046

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references