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: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 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 U S A 104: 15671

  • DOI: https://doi.org/10.1073/pnas.0707326104
  • Primary Citation of Related Structures:  
    2V7Q

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
A, B, C
510Bos taurusMutation(s): 0 
EC: 3.6.1.14
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UniProt GroupP19483
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA
D, E, F
482Bos taurusMutation(s): 0 
EC: 3.6.1.14 (PDB Primary Data), 7.1.2.2 (UniProt)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE GAMMA CHAIN272Bos taurusMutation(s): 0 
UniProt
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UniProt GroupP05631
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE DELTA CHAIN146Bos taurusMutation(s): 0 
EC: 3.6.1.14
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE EPSILON CHAIN50Bos taurusMutation(s): 0 
EC: 3.6.1.14
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATPASE INHIBITOR66Bos taurusMutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B],
O [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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Q [auth D],
T [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

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S [auth E]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

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L [auth A],
N [auth B],
P [auth C],
R [auth D],
U [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 262.534α = 90
b = 103.271β = 90
c = 135.559γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view detailsBest fitted ADPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description