2WSS

The structure of the membrane extrinsic region of bovine ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

Starting Model: experimental
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Literature

The Structure of the Membrane Extrinsic Region of Bovine ATP Synthase

Rees, D.M.Leslie, A.G.W.Walker, J.E.

(2009) Proc Natl Acad Sci U S A 106: 21597

  • DOI: https://doi.org/10.1073/pnas.0910365106
  • Primary Citation of Related Structures:  
    2WSS

  • PubMed Abstract: 

    The structure of the complex between bovine mitochondrial F(1)-ATPase and a stator subcomplex has been determined at a resolution of 3.2 A. The resolved region of the stator contains residues 122-207 of subunit b; residues 5-25 and 35-57 of F(6); 3 segments of subunit d from residues 30-40, 65-74, and 85-91; and residues 1-146 and 169-189 of the oligomycin sensitivity conferral protein (OSCP). The stator subcomplex represents its membrane distal part, and its structure has been augmented with an earlier structure of a subcomplex containing residues 79-183, 3-123, and 5-70 of subunits b, d, and F(6), respectively, which extends to the surface of the inner membrane of the mitochondrion. The N-terminal domain of the OSCP links the stator with F(1)-ATPase via alpha-helical interactions with the N-terminal region of subunit alpha(E). Its C-terminal domain makes extensive helix-helix interactions with the C-terminal alpha-helix of subunit b from residues 190-207. Subunit b extends as a continuous 160-A long alpha-helix from residue 188 back to residue 79 near to the surface of the inner mitochondrial membrane. This helix appears to be stiffened by other alpha-helices in subunits d and F(6), but the structure can bend inward toward the F(1) domain around residue 146 of subunit b. The linker region between the 2 domains of the OSCP also appears to be flexible, enabling the stator to adjust its shape as it passes over the changing profile of the F(1) domain during a catalytic cycle. The structure of the membrane extrinsic part of bovine ATP synthase is now complete.


  • Organizational Affiliation

    Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/Medical Research Council Building, Hills Road, Cambridge CB2 0XY, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
A, B, C, J, K
A, B, C, J, K, L
510Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP19483
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
D, E, F, M, N
D, E, F, M, N, O
482Bos taurusMutation(s): 0 
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
G, P
272Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
H, Q
146Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
I, R
50Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP05632
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
S, W
190Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL
T, X
116Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL118Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIALV,
Y [auth Z]
76Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

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BA [auth B]
DA [auth C]
HA [auth F]
JA [auth J]
LA [auth K]
BA [auth B],
DA [auth C],
HA [auth F],
JA [auth J],
LA [auth K],
NA [auth L],
RA [auth O],
Z [auth A]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ADP
Query on ADP

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FA [auth D],
PA [auth M]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

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AA [auth A]
CA [auth B]
EA [auth C]
GA [auth D]
IA [auth F]
AA [auth A],
CA [auth B],
EA [auth C],
GA [auth D],
IA [auth F],
KA [auth J],
MA [auth K],
OA [auth L],
QA [auth M],
SA [auth O]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
S, W
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.244α = 90
b = 231.245β = 90
c = 286.361γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary