2D00

Subunit F of V-type ATPase/synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a central stalk subunit F of prokaryotic V-type ATPase/synthase from Thermus thermophilus

Makyio, H.Iino, R.Ikeda, C.Imamura, H.Tamakoshi, M.Iwata, M.Stock, D.Bernal, R.A.Carpenter, E.P.Yoshida, M.Yokoyama, K.Iwata, S.

(2005) Embo J. 24: 3974-3983

  • DOI: 10.1038/sj.emboj.7600859

  • PubMed Abstract: 
  • The crystal structure of subunit F of vacuole-type ATPase/synthase (prokaryotic V-ATPase) was determined to of 2.2 A resolution. The subunit reveals unexpected structural similarity to the response regulator proteins that include the Escherichia coli ...

    The crystal structure of subunit F of vacuole-type ATPase/synthase (prokaryotic V-ATPase) was determined to of 2.2 A resolution. The subunit reveals unexpected structural similarity to the response regulator proteins that include the Escherichia coli chemotaxis response regulator CheY. The structure was successfully placed into the low-resolution EM structure of the prokaryotic holo-V-ATPase at a location indicated by the results of crosslinking experiments. The crystal structure, together with the single-molecule analysis using fluorescence resonance energy transfer, showed that the subunit F exhibits two conformations, a 'retracted' form in the absence and an 'extended' form in the presence of ATP. Our results postulated that the subunit F is a regulatory subunit in the V-ATPase.


    Organizational Affiliation

    ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yokohama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V-type ATP synthase subunit F
A, B, C, D, E, F
109Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: atpF (vatF)
Find proteins for P74903 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P74903
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.705α = 90.00
b = 138.295β = 90.00
c = 66.096γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MLPHAREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance