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: 3.1 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


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.USA 112: 6009-6014

  • DOI: 10.1073/pnas.1506465112
  • Primary Citation of Related Structures:  

  • 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 t ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alpha, mitochondrial
A, B, C
510Bos taurusMutation(s): 0 
Gene Names: ATP5F1A (ATP5A1, ATP5A2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P19483 (Bos taurus)
Go to UniProtKB:  P19483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit beta, mitochondrial
D, E, F
482Bos taurusMutation(s): 0 
Gene Names: ATP5F1B (ATP5B)
EC: 7.1.2.2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P00829 (Bos taurus)
Go to UniProtKB:  P00829
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit gamma, mitochondrial
G
273Bos taurusMutation(s): 0 
Gene Names: ATP5F1C (ATP5C, ATP5C1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05631 (Bos taurus)
Go to UniProtKB:  P05631
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit delta, mitochondrial
H
146Bos taurusMutation(s): 0 
Gene Names: ATP5F1D (ATP5D)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05630 (Bos taurus)
Go to UniProtKB:  P05630
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit epsilon, mitochondrial
I
50Bos taurusMutation(s): 0 
Gene Names: ATP5F1E (ATP5E)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-ATPase from bovine heart mitochondria
Find proteins for P05632 (Bos taurus)
Go to UniProtKB:  P05632
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ANP
Query on ANP

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Download CCD File 
A, B, C, D, F
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TS6
Query on TS6

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Download CCD File 
E
Monothiophosphate
phosphorothioic O,O,S-acid
H3 O3 P S
RYYWUUFWQRZTIU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.353α = 90.00
b = 123.052β = 90.00
c = 261.276γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
Aimlessdata scaling
REFMACrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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