2JDI

Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase crystallised in the absence of azide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ground State Structure of F1-ATPase from Bovine Heart Mitochondria at 1.9 A Resolution

Bowler, M.W.Montgomery, M.G.Leslie, A.G.W.Walker, J.E.

(2007) J.Biol.Chem. 282: 14238

  • DOI: 10.1074/jbc.M700203200

  • PubMed Abstract: 
  • The structure of bovine F(1)-ATPase, crystallized in the presence of AMP-PNP and ADP, but in the absence of azide, has been determined at 1.9A resolution. This structure has been compared with the previously described structure of bovine F(1)-ATPase ...

    The structure of bovine F(1)-ATPase, crystallized in the presence of AMP-PNP and ADP, but in the absence of azide, has been determined at 1.9A resolution. This structure has been compared with the previously described structure of bovine F(1)-ATPase determined at 1.95A resolution with crystals grown under the same conditions but in the presence of azide. The two structures are extremely similar, but they differ in the nucleotides that are bound to the catalytic site in the beta(DP)-subunit. In the present structure, the nucleotide binding sites in the beta(DP)- and beta(TP)-subunits are both occupied by AMP-PNP, whereas in the earlier structure, the beta(TP) site was occupied by AMP-PNP and the beta(DP) site by ADP, where its binding is enhanced by a bound azide ion. Also, the conformation of the side chain of the catalytically important residue, alphaArg-373 differs in the beta(DP)- and beta(TP)-subunits. Thus, the structure with bound azide represents the ADP inhibited state of the enzyme, and the new structure represents a ground state intermediate in the active catalytic cycle of ATP hydrolysis.


    Organizational Affiliation

    The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
A, B, C
510Bos taurusMutation(s): 0 
Gene Names: ATP5F1A (ATP5A1, ATP5A2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P19483 (Bos taurus)
Go to UniProtKB:  P19483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT BETA
D, E, F
482Bos taurusMutation(s): 0 
Gene Names: ATP5F1B (ATP5B)
EC: 7.1.2.2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P00829 (Bos taurus)
Go to UniProtKB:  P00829
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE GAMMA CHAIN
G
273Bos taurusMutation(s): 0 
Gene Names: ATP5F1C (ATP5C, ATP5C1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05631 (Bos taurus)
Go to UniProtKB:  P05631
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE DELTA CHAIN
H
146Bos taurusMutation(s): 0 
Gene Names: ATP5F1D (ATP5D)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05630 (Bos taurus)
Go to UniProtKB:  P05630
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE EPSILON CHAIN
I
50Bos taurusMutation(s): 0 
Gene Names: ATP5F1E (ATP5E)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05632 (Bos taurus)
Go to UniProtKB:  P05632
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D, F
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.610α = 90.00
b = 123.130β = 90.00
c = 261.760γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Refinement description, Version format compliance