4B2Q

Model of the yeast F1Fo-ATP synthase dimer based on subtomogram average


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 37.0 Å
  • Aggregation State: CELL 
  • Reconstruction Method: TOMOGRAPHY 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the Yeast F1Fo-ATP Synthase Dimer and its Role in Shaping the Mitochondrial Cristae.

Davies, K.M.Anselmi, C.Wittig, I.Faraldo-Gomez, J.D.Kuhlbrandt, W.

(2012) Proc Natl Acad Sci U S A 109: 13602

  • DOI: https://doi.org/10.1073/pnas.1204593109
  • Primary Citation of Related Structures:  
    4B2Q

  • PubMed Abstract: 

    We used electron cryotomography of mitochondrial membranes from wild-type and mutant Saccharomyces cerevisiae to investigate the structure and organization of ATP synthase dimers in situ. Subtomogram averaging of the dimers to 3.7 nm resolution revealed a V-shaped structure of twofold symmetry, with an angle of 86° between monomers. The central and peripheral stalks are well resolved. The monomers interact within the membrane at the base of the peripheral stalks. In wild-type mitochondria ATP synthase dimers are found in rows along the highly curved cristae ridges, and appear to be crucial for membrane morphology. Strains deficient in the dimer-specific subunits e and g or the first transmembrane helix of subunit 4 lack both dimers and lamellar cristae. Instead, cristae are either absent or balloon-shaped, with ATP synthase monomers distributed randomly in the membrane. Computer simulations indicate that isolated dimers induce a plastic deformation in the lipid bilayer, which is partially relieved by their side-by-side association. We propose that the assembly of ATP synthase dimer rows is driven by the reduction in the membrane elastic energy, rather than by direct protein contacts, and that the dimer rows enable the formation of highly curved ridges in mitochondrial cristae.


  • Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIALA,
C,
X [auth a],
Z [auth c]
485Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP07251
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIALB,
Y [auth b]
486Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP07251
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIALAA [auth d],
D
470Saccharomyces cerevisiaeMutation(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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIALBA [auth e],
CA [auth f],
E,
F
473Saccharomyces cerevisiaeMutation(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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIALDA [auth g],
G
278Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIALEA [auth h],
H
132Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIALFA [auth i],
I
59Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL76Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT B, MITOCHONDRIALQA [auth t],
T
129Bos taurusMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT D, MITOCHONDRIALRA [auth u],
U
120Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIALSA [auth v],
V
66Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT O, MITOCHONDRIALTA [auth w],
W
120Bos taurusMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
EB [auth a]
GB [auth b]
IB [auth c]
UA [auth A]
WA [auth B]
EB [auth a],
GB [auth b],
IB [auth c],
UA [auth A],
WA [auth B],
YA [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AB [auth D],
CB [auth F],
KB [auth d],
MB [auth f]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BB [auth D]
DB [auth F]
FB [auth a]
HB [auth b]
JB [auth c]
BB [auth D],
DB [auth F],
FB [auth a],
HB [auth b],
JB [auth c],
LB [auth d],
NB [auth f],
VA [auth A],
XA [auth B],
ZA [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 37.0 Å
  • Aggregation State: CELL 
  • Reconstruction Method: TOMOGRAPHY 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMOD

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Derived calculations
  • Version 1.3: 2017-08-23
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description