5FIL | pdb_00005fil

Bovine mitochondrial ATP synthase state 3b


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM.

Zhou, A.Rohou, A.Schep, D.G.Bason, J.V.Montgomery, M.G.Walker, J.E.Grigorieff, N.Rubinstein, J.L.

(2015) Elife 4: e10180-e10180

  • DOI: https://doi.org/10.7554/eLife.10180
  • Primary Citation Related Structures: 
    5ARA, 5ARE, 5ARH, 5ARI, 5FIJ, 5FIK, 5FIL

  • PubMed Abstract: 

    Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.


  • Organizational Affiliation
    • The Hospital for Sick Children Research Institute, Toronto, Canada.

Macromolecule Content 

  • Total Structure Weight: 518.89 kDa 
  • Atom Count: 18,546 
  • Modeled Residue Count: 4,641 
  • Deposited Residue Count: 4,803 
  • Unique protein chains: 11

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
A, B, C
510Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19483 (Bos taurus)
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UniProt GroupP19483
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
D, E, F
482Bos taurusMutation(s): 0 
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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UniProt GroupP00829
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL273Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05631 (Bos taurus)
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UniProt GroupP05631
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL146Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05630 (Bos taurus)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL50Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05632 (Bos taurus)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE F(0) COMPLEX SUBUNIT C1, MITOCHONDRIAL
J, K, L, M, N
J, K, L, M, N, O, P, Q
72Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32876 (Bos taurus)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT O, MITOCHONDRIALR [auth S]190Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13621 (Bos taurus)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIALS [auth T]174Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13619 (Bos taurus)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT D, MITOCHONDRIALT [auth U]124Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIALU [auth V]77Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02721 (Bos taurus)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIALV [auth W]217Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00847 (Bos taurus)
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description