Crystal Structure of subunit C (vma5p) of the yeast V-ATPase

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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This is version 1.4 of the entry. See complete history


Crystal structure of yeast V-ATPase subunit C reveals its stator function

Drory, O.Frolow, F.Nelson, N.

(2004) EMBO Rep 5: 1148-1152

  • DOI: https://doi.org/10.1038/sj.embor.7400294
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Vacuolar H(+)-ATPase (V-ATPase) has a crucial role in the vacuolar system of eukaryotic cells. It provides most of the energy required for transport systems that utilize the proton-motive force that is generated by ATP hydrolysis. Some, but not all, of the V-ATPase subunits are homologous to those of F-ATPase and the nonhomologous subunits determine the unique features of V-ATPase. We determined the crystal structure of V-ATPase subunit C (Vma5p), which does not show any homology with F-ATPase subunits, at 1.75 A resolution. The structural features suggest that subunit C functions as a flexible stator that holds together the catalytic and membrane sectors of the enzyme. A second crystal form that was solved at 2.9 A resolution supports the flexible nature of subunit C. These structures provide a framework for exploring the unique mechanistic features of V-ATPases.

  • Organizational Affiliation

    Department of Biochemistry, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar ATP synthase subunit C392Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VMA5
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31412 
Go to UniProtKB:  P31412
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31412
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TLA

Download Ideal Coordinates CCD File 
C4 H6 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.537α = 90
b = 62.537β = 90
c = 337.375γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-03-20
    Changes: Refinement description