2V7Q

The structure of F1-ATPase inhibited by I1-60HIS, a monomeric form of the inhibitor protein, IF1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

How the Regulatory Protein, If1, Inhibits F1- ATPase from Bovine Mitochondria.

Gledhill, J.R.Montgomery, M.G.Leslie, A.G.W.Walker, J.E.

(2007) Proc.Natl.Acad.Sci.USA 104: 15671

  • DOI: 10.1073/pnas.0707326104

  • PubMed Abstract: 
  • The structure of bovine F(1)-ATPase inhibited by a monomeric form of the inhibitor protein, IF(1), known as I1-60His, lacking most of the dimerization region, has been determined at 2.1-A resolution. The resolved region of the inhibitor from residues ...

    The structure of bovine F(1)-ATPase inhibited by a monomeric form of the inhibitor protein, IF(1), known as I1-60His, lacking most of the dimerization region, has been determined at 2.1-A resolution. The resolved region of the inhibitor from residues 8-50 consists of an extended structure from residues 8-13, followed by two alpha-helices from residues 14-18 and residues 21-50 linked by a turn. The binding site in the beta(DP)-alpha(DP) catalytic interface is complex with contributions from five different subunits of F(1)-ATPase. The longer helix extends from the external surface of F(1) via a deep groove made from helices and loops in the C-terminal domains of subunits beta(DP), alpha(DP), beta(TP), and alpha(TP) to the internal cavity surrounding the central stalk. The linker and shorter helix interact with the gamma-subunit in the central stalk, and the N-terminal region extends across the central cavity to interact with the nucleotide binding domain of the alpha(E) subunit. To form these complex interactions and penetrate into the core of the enzyme, it is likely that the initial interaction of the inhibitor with F(1) forms via the open conformation of the beta(E) subunit. Then, as two ATP molecules are hydrolyzed, the beta(E)-alpha(E) interface converts to the beta(DP)-alpha(DP) interface via the beta(TP)-alpha(TP) interface, trapping the inhibitor progressively in its binding site and a nucleotide in the catalytic site of subunit beta(DP). The inhibition probably arises by IF(1) imposing the structure and properties of the beta(TP)-alpha(TP) interface on the beta(DP)-alpha(DP) interface, thereby preventing it from hydrolyzing the bound ATP.


    Organizational Affiliation

    Medical Research Council Dunn Human Nutrition Unit, Cambridge CB2 0XY, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
A, B, C
510Bos taurusMutation(s): 0 
Gene Names: ATP5F1A (ATP5A1, ATP5A2)
Find proteins for P19483 (Bos taurus)
Go to UniProtKB:  P19483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT BETA
D, E, F
482Bos taurusMutation(s): 0 
Gene Names: ATP5F1B (ATP5B)
EC: 7.1.2.2
Find proteins for P00829 (Bos taurus)
Go to UniProtKB:  P00829
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE GAMMA CHAIN
G
272Bos taurusMutation(s): 0 
Gene Names: ATP5F1C (ATP5C, ATP5C1)
Find proteins for P05631 (Bos taurus)
Go to UniProtKB:  P05631
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE DELTA CHAIN
H
146Bos taurusMutation(s): 0 
Gene Names: ATP5F1D (ATP5D)
Find proteins for P05630 (Bos taurus)
Go to UniProtKB:  P05630
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE EPSILON CHAIN
I
50Bos taurusMutation(s): 0 
Gene Names: ATP5F1E (ATP5E)
Find proteins for P05632 (Bos taurus)
Go to UniProtKB:  P05632
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATPASE INHIBITOR
J
66Bos taurusMutation(s): 0 
Gene Names: ATP5IF1 (ATPI, ATPIF1)
Find proteins for P01096 (Bos taurus)
Go to UniProtKB:  P01096
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
D, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 262.534α = 90.00
b = 103.271β = 90.00
c = 135.559γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance