1H8E

(ADP.AlF4)2(ADP.SO4) bovine F1-ATPase (all three catalytic sites occupied)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 

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This is version 1.2 of the entry. See complete history. 


Literature

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

  • DOI: https://doi.org/10.1016/s0092-8674(01)00452-4
  • Primary Citation of Related Structures:  
    1H8E

  • PubMed Abstract: 

    • The crystal structure of a novel aluminium fluoride inhibited form of bovine mitochondrial F(1)-ATPase has been determined at 2 A resolution. In contrast to all previously determined structures of the bovine enzyme, all three catalytic sites are occupied by nucleotide ...

    The crystal structure of a novel aluminium fluoride inhibited form of bovine mitochondrial F(1)-ATPase has been determined at 2 A resolution. In contrast to all previously determined structures of the bovine enzyme, all three catalytic sites are occupied by nucleotide. The subunit that did not bind nucleotide in previous structures binds ADP and sulfate (mimicking phosphate), and adopts a "half-closed" conformation. This structure probably represents the posthydrolysis, pre-product release step on the catalytic pathway. A catalytic scheme for hydrolysis (and synthesis) at physiological rates and a mechanism for the ATP-driven rotation of the gamma subunit are proposed based on the crystal structures of the bovine enzyme.

    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 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: 2309
    • 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: 

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASEA, B, C510Bos taurusMutation(s): 1 
Gene Names: ATP5F1A, ATP5A1, ATP5A2
UniProt
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Go to UniProtKB:  P19483
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UniProt GroupP19483
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASED, E, F482Bos taurusMutation(s): 0 
Gene Names: ATP5F1B, ATP5B
EC: 7.1.2.2
UniProt
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UniProt GroupP00829
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASEG272Bos taurusMutation(s): 0 
Gene Names: ATP5F1C, ATP5C, ATP5C1
UniProt
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UniProt GroupP05631
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASEH146Bos taurusMutation(s): 0 
Gene Names: ATP5F1D, ATP5D
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UniProt GroupP05630
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASEI50Bos taurusMutation(s): 0 
Gene Names: ATP5F1E, ATP5E
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UniProt GroupP05632
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
J [auth A],
M [auth B],
Q [auth C],
T [auth D],
W [auth E],
J [auth A],
M [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ALF
Query on ALF
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BA [auth F],
V [auth D]		TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
Y [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
L [auth A],
O [auth B],
P [auth B],
S [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth F],
K [auth A],
N [auth B],
R [auth C],
U [auth D],
AA [auth F],
K [auth A],
N [auth B],
R [auth C],
U [auth D],
X [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 267.7α = 90
b = 106.2β = 90
c = 138.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance