4YXW

Bovine heart mitochondrial F1-ATPase inhibited by AMP-PNP and ADP in the presence of thiophosphate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

How release of phosphate from mammalian F1-ATPase generates a rotary substep.

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

(2015) Proc Natl Acad Sci U S A 112: 6009-6014

  • DOI: 10.1073/pnas.1506465112
  • Primary Citation of Related Structures:  
    4Z1M, 4YXW

  • PubMed Abstract: 
  • The rotation of the central stalk of F1-ATPase is driven by energy derived from the sequential binding of an ATP molecule to its three catalytic sites and the release of the products of hydrolysis. In human F1-ATPase, each 360° rotation consists of three 120° steps composed of substeps of about 65°, 25°, and 30°, with intervening ATP binding, phosphate release, and catalytic dwells, respectively ...

    The rotation of the central stalk of F1-ATPase is driven by energy derived from the sequential binding of an ATP molecule to its three catalytic sites and the release of the products of hydrolysis. In human F1-ATPase, each 360° rotation consists of three 120° steps composed of substeps of about 65°, 25°, and 30°, with intervening ATP binding, phosphate release, and catalytic dwells, respectively. The F1-ATPase inhibitor protein, IF1, halts the rotary cycle at the catalytic dwell. The human and bovine enzymes are essentially identical, and the structure of bovine F1-ATPase inhibited by IF1 represents the catalytic dwell state. Another structure, described here, of bovine F1-ATPase inhibited by an ATP analog and the phosphate analog, thiophosphate, represents the phosphate binding dwell. Thiophosphate is bound to a site in the α(E)β(E)-catalytic interface, whereas in F1-ATPase inhibited with IF1, the equivalent site is changed subtly and the enzyme is incapable of binding thiophosphate. These two structures provide a molecular mechanism of how phosphate release generates a rotary substep as follows. In the active enzyme, phosphate release from the β(E)-subunit is accompanied by a rearrangement of the structure of its binding site that prevents released phosphate from rebinding. The associated extrusion of a loop in the β(E)-subunit disrupts interactions in the α(E)β(E-)catalytic interface and opens it to its fullest extent. Other rearrangements disrupt interactions between the γ-subunit and the C-terminal domain of the α(E)-subunit. To restore most of these interactions, and to make compensatory new ones, the γ-subunit rotates through 25°-30°.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alpha, mitochondrialA, B, C510Bos taurusMutation(s): 2 
Gene Names: ATP5F1AATP5A1ATP5A2
Membrane Entity: Yes 
UniProt
Find proteins for P19483 (Bos taurus)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit beta, mitochondrialD, E, F482Bos taurusMutation(s): 0 
Gene Names: ATP5F1BATP5B
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00829 (Bos taurus)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit gamma, mitochondrialG273Bos taurusMutation(s): 0 
Gene Names: ATP5F1CATP5CATP5C1
Membrane Entity: Yes 
UniProt
Find proteins for P05631 (Bos taurus)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit delta, mitochondrialH146Bos taurusMutation(s): 0 
Gene Names: ATP5F1DATP5D
Membrane Entity: Yes 
UniProt
Find proteins for P05630 (Bos taurus)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit epsilon, mitochondrialI50Bos taurusMutation(s): 0 
Gene Names: ATP5F1EATP5E
Membrane Entity: Yes 
UniProt
Find proteins for P05632 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
J [auth A], L [auth B], N [auth C], P [auth D], T [auth F]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
TS6
Query on TS6

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S [auth E]Monothiophosphate
H3 O3 P S
RYYWUUFWQRZTIU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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R [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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K [auth A], M [auth B], O [auth C], Q [auth D], U [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
V [auth F]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.353α = 90
b = 123.052β = 90
c = 261.276γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-05-20
    Changes: Database references