1U7L | pdb_00001u7l

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

• PDB DOI: https://doi.org/10.2210/pdb1U7L/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-04 Released: 2004-11-23 
• Deposition Author(s): Nelson, N., Frolow, F., Drory, O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

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

Drory, O., Frolow, F., Nelson, N.

(2004) EMBO Rep 5: 1148-1152

• PubMed: 15540116 
• DOI: https://doi.org/10.1038/sj.embor.7400294
• Primary Citation Related Structures: 
  1U7L


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.39 kDa 
• Atom Count: 3,428 
• Modeled Residue Count: 364 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar ATP synthase subunit C	A	392	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: VMA5 EC: 3.6.3.14
UniProt
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31412  Go to UniProtKB:  P31412

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.537	α = 90
b = 62.537	β = 90
c = 337.375	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-23 
Deposition Author(s): Nelson, N., Frolow, F., Drory, O.

Revision History  

• 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