1W0J

Beryllium fluoride inhibited bovine F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/sj.emboj.7600293
  • Primary Citation of Related Structures:  
    1W0J, 1W0K

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE ALPHA CHAIN HEART ISOFORM, MITOCHONDRIAL PRECURSOR
A, B, C
510Bos taurusMutation(s): 0 
EC: 3.6.3.14
UniProt
Find proteins for P19483 (Bos taurus)
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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
ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR
D, E, F
482Bos taurusMutation(s): 0 
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
UniProt
Find proteins for P00829 (Bos taurus)
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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
ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR272Bos taurusMutation(s): 0 
EC: 3.6.3.14
UniProt
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
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UniProt GroupP05631
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
N [auth C],
R [auth D],
V [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

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U [auth E]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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J [auth A],
M [auth B],
P [auth C],
Q [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BEF
Query on BEF

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T [auth D],
X [auth F]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 283.52α = 90
b = 107.374β = 90
c = 137.936γ = 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: 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: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description