1W0J

Beryllium fluoride inhibited bovine F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  
  • Also Cited By: 2CK3

  • 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: 
    • 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.Mol.Biol. 7: 1055
    • 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
    • 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
    • Molecular Architecture of the Rotary Motor in ATP Synthase
      Stock, D.,Leslie, A.G.W.,Walker, J.E.
      (1999) Science 286: 1700
    • 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
    • ATP Synthesis by Rotary Catalysis (Nobel Lecture)
      Walker, J.E.
      (1998) Angew.Chem.Int.Ed.Engl. 37: 2308


    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: ATP5F1A (ATP5A1, ATP5A2)
Find proteins for P19483 (Bos taurus)
Go to UniProtKB:  P19483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR
D, E, F
482Bos taurusMutation(s): 0 
Gene Names: ATP5F1B (ATP5B)
EC: 7.1.2.2
Find proteins for P00829 (Bos taurus)
Go to UniProtKB:  P00829
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR
G
272Bos taurusMutation(s): 0 
Gene Names: ATP5F1C (ATP5C, ATP5C1)
Find proteins for P05631 (Bos taurus)
Go to UniProtKB:  P05631
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

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

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Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

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Download CCD File 
D, F
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 283.520α = 90.00
b = 107.374β = 90.00
c = 137.936γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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