1EFR

BOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH THE PEPTIDE ANTIBIOTIC EFRAPEPTIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The Structure of Bovine F1-ATPase Complexed with the Peptide Antibiotic Efrapeptin.

Abrahams, J.P.Buchanan, S.K.Van Raaij, M.J.Fearnley, I.M.Leslie, A.G.Walker, J.E.

(1996) Proc Natl Acad Sci U S A 93: 9420

  • DOI: 10.1073/pnas.93.18.9420
  • Primary Citation of Related Structures:  
    1EFR

  • PubMed Abstract: 
  • In the previously determined structure of mitochondrial F1-ATPase 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 ...

    In the previously determined structure of mitochondrial F1-ATPase 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. AMP-PNP and ADP are bound to subunits beta TP and beta DP, respectively, and the third beta-subunit (beta E) has no bound nucleotide. The efrapeptins are a closely related family of modified linear peptides containing 15 amino acids that inhibit both ATP synthesis and hydrolysis by binding to the F1 catalytic domain of F1F0-ATP synthase. In crystals of F1-ATPase grown in the presence of both nucleotides and inhibitor, efrapeptin is bound to a unique site in the central cavity of the enzyme. Its binding is associated with small structural changes in side chains of F1-ATPase around the binding pocket. Efrapeptin makes hydrophobic contacts with the alpha-helical structure in the gamma-subunit, which traverses the cavity, and with subunit beta E and the two adjacent alpha-subunits. Two intermolecular hydrogen bonds could also form. Intramolecular hydrogen bonds probably help to stabilize efrapeptin's two domains (residues 1-6 and 9-15, respectively), which are connected by a flexible region (beta Ala-7 and Gly-8). Efrapeptin appears to inhibit F1-ATPase by blocking the conversion of subunit beta E to a nucleotide binding conformation, as would be required by an enzyme mechanism involving cyclic interconversion of catalytic sites.


    Related Citations: 
    • 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
    • Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria
      Abrahams, J.P., Leslie, A.G., 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
    • Inherent Asymmetry of the Structure of F1-ATPase from Bovine Heart Mitochondria at 6.5 A Resolution
      Abrahams, J.P., Lutter, R., Todd, R.J., Van Raaij, M.J., Leslie, A.G., Walker, J.E.
      (1993) EMBO J 12: 1775

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT ALPHAA, B, C510Bos taurusMutation(s): 0 
Gene Names: ATP5F1AATP5A1ATP5A2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with peptide antibiotic efrapeptin
Find proteins for P19483 (Bos taurus)
Explore P19483 
Go to UniProtKB:  P19483
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT BETAD, E, F482Bos taurusMutation(s): 0 
Gene Names: ATP5F1BATP5B
EC: 7.1.2.2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with peptide antibiotic efrapeptin
Find proteins for P00829 (Bos taurus)
Explore P00829 
Go to UniProtKB:  P00829
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT GAMMAG272Bos taurusMutation(s): 0 
Gene Names: ATP5F1CATP5CATP5C1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with peptide antibiotic efrapeptin
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
EFRAPEPTIN CQ17Tolypocladium inflatumMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase complexed with peptide antibiotic efrapeptin
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 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
MG
Query on MG

Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AIB
Query on AIB
QL-PEPTIDE LINKINGC4 H9 N O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000186
Query on PRD_000186
QEFRAPEPTIN CPolypeptide /  Antimicrobial

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 285.7α = 90
b = 107.4β = 90
c = 139.5γ = 90
Software Package:
Software NamePurpose
CCP4model building
TNTrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2017-11-01
    Changes: Advisory, Derived calculations, Other