4TSF

The Pathway of Binding of the Intrinsically Disordered Mitochondrial Inhibitor Protein to F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Pathway of binding of the intrinsically disordered mitochondrial inhibitor protein to F1-ATPase.

Bason, J.V.Montgomery, M.G.Leslie, A.G.Walker, J.E.

(2014) Proc Natl Acad Sci U S A 111: 11305

  • DOI: 10.1073/pnas.1411560111
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The hydrolysis of ATP by the ATP synthase in mitochondria is inhibited by a protein called IF1. Bovine IF1 has 84 amino acids, and its N-terminal inhibitory region is intrinsically disordered. In a known structure of bovine F1-ATPase inhibited with r ...

    The hydrolysis of ATP by the ATP synthase in mitochondria is inhibited by a protein called IF1. Bovine IF1 has 84 amino acids, and its N-terminal inhibitory region is intrinsically disordered. In a known structure of bovine F1-ATPase inhibited with residues 1-60 of IF1, the inhibitory region from residues 1-50 is mainly α-helical and buried deeply at the α(DP)β(DP)-catalytic interface, where it forms extensive interactions with five of the nine subunits of F1-ATPase but mainly with the β(DP)-subunit. As described here, on the basis of two structures of inhibited complexes formed in the presence of large molar excesses of residues 1-60 of IF1 and of a version of IF1 with the mutation K39A, it appears that the intrinsically disordered inhibitory region interacts first with the αEβE-catalytic interface, the most open of the three catalytic interfaces, where the available interactions with the enzyme allow it to form an α-helix from residues 31-49. Then, in response to the hydrolysis of an ATP molecule and the associated partial closure of the interface to the αTPβTP state, the extent of the folded α-helical region of IF1 increases to residues 23-50 as more interactions with the enzyme become possible. Finally, in response to the hydrolysis of a second ATP molecule and a concomitant 120° rotation of the γ-subunit, the interface closes further to the α(DP)β(DP)-state, allowing more interactions to form between the enzyme and IF1. The structure of IF1 now extends to its maximally folded state found in the previously observed inhibited complex.


    Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom; and walker@mrc-mbu.cam.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alpha, mitochondrialA, B, C510Bos taurusMutation(s): 0 
Gene Names: ATP5F1AATP5A1ATP5A2
Find proteins for P19483 (Bos taurus)
Explore P19483 
Go to UniProtKB:  P19483
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit beta, mitochondrialD, E, F480Bos taurusMutation(s): 0 
Gene Names: ATP5F1BATP5B
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Find proteins for P00829 (Bos taurus)
Explore P00829 
Go to UniProtKB:  P00829
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit gamma, mitochondrialG273Bos taurusMutation(s): 0 
Gene Names: ATP5F1CATP5CATP5C1
Find proteins for P05631 (Bos taurus)
Explore P05631 
Go to UniProtKB:  P05631
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATPase inhibitor, mitochondrialH, I66Bos taurusMutation(s): 0 
Gene Names: ATPIF1ATPIATP5IF1
Find proteins for P01096 (Bos taurus)
Explore P01096 
Go to UniProtKB:  P01096
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download CCD File 
D, F
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.015α = 90
b = 154.42β = 90
c = 269.465γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references