2XND

Crystal structure of bovine F1-c8 sub-complex of ATP Synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bioenergetic Cost of Making an Adenosine Triphosphate Molecule in Animal Mitochondria.

Watt, I.N.Montgomery, M.G.Runswick, M.J.Leslie, A.G.W.Walker, J.E.

(2010) Proc.Natl.Acad.Sci.USA 107: 16823

  • DOI: 10.1073/pnas.1011099107

  • PubMed Abstract: 
  • The catalytic domain of the F-ATPase in mitochondria protrudes into the matrix of the organelle, and is attached to the membrane domain by central and peripheral stalks. Energy for the synthesis of ATP from ADP and phosphate is provided by the transm ...

    The catalytic domain of the F-ATPase in mitochondria protrudes into the matrix of the organelle, and is attached to the membrane domain by central and peripheral stalks. Energy for the synthesis of ATP from ADP and phosphate is provided by the transmembrane proton-motive-force across the inner membrane, generated by respiration. The proton-motive force is coupled mechanically to ATP synthesis by the rotation at about 100 times per second of the central stalk and an attached ring of c-subunits in the membrane domain. Each c-subunit carries a glutamate exposed around the midpoint of the membrane on the external surface of the ring. The rotation is generated by protonation and deprotonation successively of each glutamate. Each 360° rotation produces three ATP molecules, and requires the translocation of one proton per glutamate by each c-subunit in the ring. In fungi, eubacteria, and plant chloroplasts, ring sizes of c(10)-c(15) subunits have been observed, implying that these enzymes need 3.3-5 protons to make each ATP, but until now no higher eukaryote has been examined. As shown here in the structure of the bovine F(1)-c-ring complex, the c-ring has eight c-subunits. As the sequences of c-subunits are identical throughout almost all vertebrates and are highly conserved in invertebrates, their F-ATPases probably contain c(8)-rings also. Therefore, in about 50,000 vertebrate species, and probably in many or all of the two million invertebrate species, 2.7 protons are required by the F-ATPase to make each ATP molecule.


    Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 0XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
A, B, C
492Bos taurusMutation(s): 0 
Gene Names: ATP5F1A (ATP5A1, ATP5A2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-c-ring (c8) complex
Find proteins for P19483 (Bos taurus)
Go to UniProtKB:  P19483
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
D, E, F
467Bos 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-c-ring (c8) complex
Find proteins for P00829 (Bos taurus)
Go to UniProtKB:  P00829
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
G
272Bos taurusMutation(s): 0 
Gene Names: ATP5F1C (ATP5C, ATP5C1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-c-ring (c8) complex
Find proteins for P05631 (Bos taurus)
Go to UniProtKB:  P05631
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
H
131Bos taurusMutation(s): 0 
Gene Names: ATP5F1D (ATP5D)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-c-ring (c8) complex
Find proteins for P05630 (Bos taurus)
Go to UniProtKB:  P05630
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
I
47Bos taurusMutation(s): 0 
Gene Names: ATP5F1E (ATP5E)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-c-ring (c8) complex
Find proteins for P05632 (Bos taurus)
Go to UniProtKB:  P05632
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
J, K, L, M, N, O, P, Q
72Bos taurusMutation(s): 0 
Gene Names: ATP5MC1 (ATP5G1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
F1-c-ring (c8) complex
Find proteins for P32876 (Bos taurus)
Go to UniProtKB:  P32876
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
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

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: 3.5 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 155.740α = 90.00
b = 157.100β = 90.00
c = 247.270γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Database references, Non-polymer description, Version format compliance