4EFA

Crystal Structure of the Heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase - second conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Yeast Vacuolar ATPase Heterotrimeric EGC(head) Peripheral Stalk Complex.

Oot, R.A.Huang, L.S.Berry, E.A.Wilkens, S.

(2012) Structure 20: 1881-1892

  • DOI: 10.1016/j.str.2012.08.020
  • Primary Citation of Related Structures:  
    4DL0, 4EFA

  • PubMed Abstract: 
  • Vacuolar ATPases (V-ATPases) are multisubunit rotary motor proton pumps that function to acidify subcellular organelles in all eukaryotic organisms. V-ATPase is regulated by a unique mechanism that involves reversible dissociation into V₁-ATPase and V₀ proton channel, a process that involves breaking of protein interactions mediated by subunit C, the cytoplasmic domain of subunit "a" and three "peripheral stalks," each made of a heterodimer of E and G subunits ...

    Vacuolar ATPases (V-ATPases) are multisubunit rotary motor proton pumps that function to acidify subcellular organelles in all eukaryotic organisms. V-ATPase is regulated by a unique mechanism that involves reversible dissociation into V₁-ATPase and V₀ proton channel, a process that involves breaking of protein interactions mediated by subunit C, the cytoplasmic domain of subunit "a" and three "peripheral stalks," each made of a heterodimer of E and G subunits. Here, we present crystal structures of a yeast V-ATPase heterotrimeric complex composed of EG heterodimer and the head domain of subunit C (C(head)). The structures show EG heterodimer folded in a noncanonical coiled coil that is stabilized at its N-terminal ends by binding to C(head). The coiled coil is disrupted by a bulge of partially unfolded secondary structure in subunit G and we speculate that this unique feature in the eukaryotic V-ATPase peripheral stalk may play an important role in enzyme structure and regulation by reversible dissociation.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit CA [auth C]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VAT3VATCVMA5YKL080WYKL410
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for P31412 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31412 
Go to UniProtKB:  P31412
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit GB [auth G]119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA10YHR039BCYHR039C-AYHR039C-B
EC: 3.6.3.14
UniProt
Find proteins for P48836 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P48836 
Go to UniProtKB:  P48836
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit EC [auth E]233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: O6241VAT5VMA4YOR332W
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for P22203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22203 
Go to UniProtKB:  P22203
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.234 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.537α = 90
b = 93.648β = 90
c = 116.891γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-11-28
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description