1COW

BOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH AUROVERTIN B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.

van Raaij, M.J.Abrahams, J.P.Leslie, A.G.Walker, J.E.

(1996) Proc Natl Acad Sci U S A 93: 6913-6917

  • DOI: https://doi.org/10.1073/pnas.93.14.6913
  • Primary Citation of Related Structures:  
    1COW

  • PubMed Abstract: 

    In the structure of bovine mitochondrial F1-ATPase that was previously determined with crystals grown in the presence of adenylyl-imidodiphosphate (AMP-PNP) and ADP, the three catalytic beta-subunits have different conformations and nucleotide occupancies. Adenylyl-imidodiphosphate is bound to one beta-subunit (betaTP), ADP is bound to the second (betaDP), and no nucleotide is bound to the third (betaE). Here we show that the uncompetitive inhibitor aurovertin B binds to bovine F1 at two equivalent sites in betaTP and betaE, in a cleft between the nucleotide binding and C-terminal domains. In betaDP, the aurovertin B pocket is incomplete and is inaccessible to the inhibitor. The aurovertin B bound to betaTP interacts with alpha-Glu399 in the adjacent alphaTP subunit, whereas the aurovertin B bound to betaE is too distant from alphaE to make an equivalent interaction. Both sites encompass betaArg-412, which was shown by mutational studies to be involved in binding aurovertin. Except for minor changes around the aurovertin pockets, the structure of bovine F1-ATPase is the same as determined previously. Aurovertin B appears to act by preventing closure of the catalytic interfaces, which is essential for a catalytic mechanism involving cyclic interconversion of catalytic sites.


  • Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASE
A, B, C
510Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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 
Membrane Entity: Yes 
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): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
Entity Groups  
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UniProt GroupP05631
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
M [auth C],
R [auth F]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
AUR
Query on AUR

Download Ideal Coordinates CCD File 
P [auth E],
S [auth F]
AUROVERTIN B
C25 H32 O8
QXCOFYWOWZJFEA-YJMRODJJSA-N
ADP
Query on ADP

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

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
L [auth C],
N [auth D],
Q [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.280 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 283.4α = 90
b = 107.6β = 90
c = 140.2γ = 90
Software Package:
Software NamePurpose
TNTrefinement
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-08-07
    Changes: Data collection, Other, Structure summary
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations