1H8H

Bovine mitochondrial F1-ATPase crystallised in the presence of 5mm AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure and Nucleotide Occupancy of Bovine Mitochondrial F(1)-ATPase are not Influenced by Crystallisation at High Concentrations of Nucleotide

Menz, R.I.Leslie, A.G.W.Walker, J.E.

(2001) FEBS Lett. 494: 11


  • PubMed Abstract: 
  • Analysis of tryptophan mutants of F(1)-ATPase from Escherichia coli [Löbau et al. (1997) FEBS Lett. 404, 15-18] suggested that nucleotide concentrations used to grow crystals for the determination of the structure of bovine F(1)-ATPase [Abrahams et a ...

    Analysis of tryptophan mutants of F(1)-ATPase from Escherichia coli [Löbau et al. (1997) FEBS Lett. 404, 15-18] suggested that nucleotide concentrations used to grow crystals for the determination of the structure of bovine F(1)-ATPase [Abrahams et al. (1994) Nature 370, 621-628] would be sufficient to occupy only two catalytic sites, and that higher concentrations of nucleotide would result in all three sites being occupied. We have determined the structure of bovine F(1)-ATPase at 2.9 A resolution with crystals grown in the presence of 5 mM AMPPNP and 5 microM ADP. Similar to previous structures of bovine F(1)-ATPase determined with crystals grown in the presence of lower nucleotide concentrations, only two beta-subunits have bound nucleotide and the third subunit remains empty.


    Related Citations: 
    • 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
    • Inherent Asymmetry of the Structure of F1-ATPase from Bovine Heart Mitochondria at 6.5 A Resolution
      Abrahams, J.P.,Lutter, R.,Todd, R.J.,Van Raaij, M.J.,Leslie, A.G.,Walker, J.E.
      (1993) Embo J. 12: 1775
    • 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


    Organizational Affiliation

    The Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BOVINE MITOCHONDRIAL F1-ATPASE
A, B, C
510Bos taurusGene Names: ATP5A1 (ATP5A2)
Find proteins for P19483 (Bos taurus)
Go to Gene View: ATP5A1
Go to UniProtKB:  P19483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BOVINE MITOCHONDRIAL F1-ATPASE
D, E, F
482Bos taurusGene Names: ATP5B
EC: 3.6.3.14
Find proteins for P00829 (Bos taurus)
Go to Gene View: ATP5B
Go to UniProtKB:  P00829
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BOVINE MITOCHONDRIAL F1-ATPASE
G
272Bos taurusGene Names: ATP5C1 (ATP5C)
Find proteins for P05631 (Bos taurus)
Go to Gene View: ATP5C1
Go to UniProtKB:  P05631
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, F
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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

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

Download SDF File 
Download CCD File 
B
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 280.000α = 90.00
b = 107.000β = 90.00
c = 139.100γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-15
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references, Non-polymer description, Other, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-03-29
    Type: Structure summary