1H8H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.236 

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This is version 1.3 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

  • DOI: https://doi.org/10.1016/s0014-5793(01)02302-x
  • Primary Citation of Related Structures:  
    1H8H

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASE
A, B, C
510Bos taurusMutation(s): 1 
UniProt
Find proteins for P19483 (Bos taurus)
Explore P19483 
Go to UniProtKB:  P19483
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19483
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASE
D, E, F
482Bos taurusMutation(s): 0 
UniProt
Find proteins for P00829 (Bos taurus)
Explore P00829 
Go to UniProtKB:  P00829
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UniProt GroupP00829
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASE272Bos taurusMutation(s): 1 
UniProt
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
Entity Groups  
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UniProt GroupP05631
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
M [auth C],
R [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
O [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
Q [auth E]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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L [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
N [auth C],
P [auth D],
S [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 280α = 90
b = 107β = 90
c = 139.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-15
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references, Non-polymer description, Other, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-03-29
    Changes: Structure summary
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description