2CK3

Azide inhibited bovine F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

How Azide Inhibits ATP Hydrolysis by the F-Atpases.

Bowler, M.W.Montgomery, M.G.Leslie, A.G.Walker, J.E.

(2006) Proc Natl Acad Sci U S A 103: 8646

  • DOI: 10.1073/pnas.0602915103
  • Primary Citation of Related Structures:  
    2CK3

  • PubMed Abstract: 
  • In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding ca ...

    In the structure of bovine F1-ATPase determined at 1.95-A resolution with crystals grown in the presence of ADP, 5'-adenylyl-imidodiphosphate, and azide, the azide anion interacts with the beta-phosphate of ADP and with residues in the ADP-binding catalytic subunit, betaDP. It occupies a position between the catalytically essential amino acids, beta-Lys-162 in the P loop and the "arginine finger" residue, alpha-Arg-373, similar to the site occupied by the gamma-phosphate in the ATP-binding subunit, betaTP. Its presence in the betaDP-subunit tightens the binding of the side chains to the nucleotide, enhancing its affinity and thereby stabilizing the state with bound ADP. This mechanism of inhibition appears to be common to many other ATPases, including ABC transporters, SecA, and DNA topoisomerase IIalpha. It also explains the stimulatory effect of azide on ATP-sensitive potassium channels by enhancing the binding of ADP.


    Related Citations: 
    • Reproducible Improvements in Order and Diffraction Limit of Crystals of Bovine Mitochondrial F(1)- ATPase by Controlled Dehydration.
      Bowler, M.W., Montgomery, M.G., Leslie, A.G., Walker, J.E.
      (2006) Acta Crystallogr D Biol Crystallogr 62: 991
    • 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
    • Tructure 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

    Dunn Human Nutrition Unit, Medical Research Council, Hills Road, Cambridge CB2 2XY, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIALABC510Bos taurusMutation(s): 0 
Gene Names: ATP5F1AATP5A1ATP5A2
EC: 3.6.3.14
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with azide
Find proteins for P19483 (Bos taurus)
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Go to UniProtKB:  P19483
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIALDEF482Bos taurusMutation(s): 0 
Gene Names: ATP5F1BATP5B
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with azide
Find proteins for P00829 (Bos taurus)
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Go to UniProtKB:  P00829
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIALG272Bos taurusMutation(s): 0 
Gene Names: ATP5F1CATP5CATP5C1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with azide
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIALH146Bos taurusMutation(s): 0 
Gene Names: ATP5F1DATP5D
EC: 3.6.3.14
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with azide
Find proteins for P05630 (Bos taurus)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIALI50Bos taurusMutation(s): 0 
Gene Names: ATP5F1EATP5E
EC: 3.6.3.14
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with azide
Find proteins for P05632 (Bos taurus)
Explore P05632 
Go to UniProtKB:  P05632
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
A, B, C, F
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download CCD File 
D
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
AZI
Query on AZI

Download CCD File 
D
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.16α = 90
b = 105.22β = 90
c = 122.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Refinement description, Version format compliance
  • Version 1.2: 2014-01-22
    Changes: Database references, Refinement description, Structure summary