1W0K

ADP inhibited bovine F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride

Kagawa, R.Montgomery, M.G.Braig, K.Leslie, A.G.W.Walker, J.E.

(2004) EMBO J 23: 2734

  • DOI: 10.1038/sj.emboj.7600293
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of bovine F1-ATPase inhibited with ADP and beryllium fluoride at 2.0 angstroms resolution contains two ADP.BeF3- complexes mimicking ATP, bound in the catalytic sites of the beta(TP) and beta(DP) subunits. Except for a 1 angstrom shift ...

    The structure of bovine F1-ATPase inhibited with ADP and beryllium fluoride at 2.0 angstroms resolution contains two ADP.BeF3- complexes mimicking ATP, bound in the catalytic sites of the beta(TP) and beta(DP) subunits. Except for a 1 angstrom shift in the guanidinium of alphaArg373, the conformations of catalytic side chains are very similar in both sites. However, the ordered water molecule that carries out nucleophilic attack on the gamma-phosphate of ATP during hydrolysis is 2.6 angstroms from the beryllium in the beta(DP) subunit and 3.8 angstroms away in the beta(TP) subunit, strongly indicating that the beta(DP) subunit is the catalytically active conformation. In the structure of F1-ATPase with five bound ADP molecules (three in alpha-subunits, one each in the beta(TP) and beta(DP) subunits), which has also been determined, the conformation of alphaArg373 suggests that it senses the presence (or absence) of the gamma-phosphate of ATP. Two catalytic schemes are discussed concerning the various structures of bovine F1-ATPase.


    Related Citations: 
    • Structure of Bovine Mitochondrial F1-ATPase with Nucleotide Bound to All Three Catalytic Sites; Implications for the Mechanism of Rotary Catalysis
      Menz, R.I., Walker, J.E., Leslie, A.G.W.
      (2001) Cell 106: 331
    • The Structure of the Central Stalk in Bovine F1-ATPase at 2.4A Resolution
      Gibbons, C., Montgomery, M.G., Leslie, A.G.W., Walker, J.E.
      (2000) Nat Struct Biol 7: 1055
    • Molecular Architecture of the Rotary Motor in ATP Synthase
      Stock, D., Leslie, A.G.W., Walker, J.E.
      (1999) Science 286: 1700
    • ATP Synthesis by Rotary Catalysis (Nobel Lecture)
      Walker, J.E.
      (1998) Angew Chem Int Ed Engl 37: 2308
    • Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria
      Abrahams, J.P., Leslie, A.G.W., Lutter, R., Walker, J.E.
      (1994) Nature 370: 621
    • Crystallization of F1-ATPase from Bovine Heart Mitochondria
      Lutter, R., Abrahams, J.P., Van Raaij, M.J., Todd, R.J., Lundqvist, T., Buchanan, S.K., Leslie, A.G., Walker, J.E.
      (1993) J Mol Biol 229: 787

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE ALPHA CHAIN HEART ISOFORM, MITOCHONDRIAL PRECURSOR
A, B, C
510Bos taurusMutation(s): 0 
Gene Names: ATP5F1AATP5A1ATP5A2
EC: 3.6.3.14
Find proteins for P19483 (Bos taurus)
Go to UniProtKB:  P19483
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR
D, E, F
482Bos taurusMutation(s): 0 
Gene Names: ATP5F1BATP5B
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Find proteins for P00829 (Bos taurus)
Go to UniProtKB:  P00829
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR
G
272Bos taurusMutation(s): 0 
Gene Names: ATP5F1CATP5CATP5C1
EC: 3.6.3.14
Find proteins for P05631 (Bos taurus)
Go to UniProtKB:  P05631
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B, C, D, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 283.036α = 90
b = 107.608β = 90
c = 139.644γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-08
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2014-10-01
    Changes: Structure summary