8P65 | pdb_00008p65

Cytochrome bc1 complex (Bos taurus)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A splendid molecular factory: De- and reconstruction of the mammalian respiratory chain.

Rimle, L.Phillips, B.P.Codo Costa Barra, I.M.Arnold, N.Hennebert, C.Meier, T.von Ballmoos, C.

(2025) Proc Natl Acad Sci U S A 122: e2416162122-e2416162122

  • DOI: https://doi.org/10.1073/pnas.2416162122
  • Primary Citation of Related Structures:  
    8P65

  • PubMed Abstract: 

    Mitochondrial respiratory complexes I to IV and the F 1 F o -ATP synthase (complex V) are large protein assemblies producing the universal cellular energy currency adenosine triphosphate (ATP). Individual complexes have been extensively studied in vitro, but functional co-reconstitution of several mammalian complexes into proteoliposomes, in particular, the combination of a primary pump with the ATP synthase, is less well understood. Here, we present a generic and scalable strategy to purify mammalian respiratory complexes I, III and the ATP synthase from enriched mitochondria in enzymatically fully active form, and procedures to reassemble the complexes into liposomes. A robust functionality can be shown by in situ monitoring of ATP synthesis rates and by using selected inhibitors of the respiratory chain complexes. By inclusion of cytochrome c oxidase, our procedures allowed us to reconstruct the entire mitochondrial respiratory chain (complexes I, III, IV, and V) in ubiquinone Q 10 containing liposomes, demonstrating oxidative phosphorylation by nicotinamide adenine dinucleotide hydrogen driven ATP synthesis. The system was fully coupled at all levels and was used to probe cardiolipin as an essential component to activate the mammalian respiratory chain. Structural characterization using electron cryomicroscopy allowed us to resolve apo-state complex III and complex V at high and medium resolution, respectively, using in silico particle sorting, confirming the presence of all protein subunits and cofactors in native stoichiometry and conformation. The reported findings will facilitate future endeavors to characterize or modulate these key bioenergetic processes.


  • Organizational Affiliation
    • Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern 3012, Switzerland.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA,
L [auth N]
446Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P31800 (Bos taurus)
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UniProt GroupP31800
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB,
M [auth O]
439Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23004 (Bos taurus)
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UniProt GroupP23004
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC,
N [auth P]
379Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00157 (Bos taurus)
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UniProt GroupP00157
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD,
O [auth Q]
241Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P00125 (Bos taurus)
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UniProt GroupP00125
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
P [auth R]
196Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
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UniProt GroupP13272
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F,
Q [auth S]
111Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00129 (Bos taurus)
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UniProt GroupP00129
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G,
R [auth T]
82Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13271 (Bos taurus)
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UniProt GroupP13271
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH,
S [auth U]
78Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00126 (Bos taurus)
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UniProt GroupP00126
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9I,
T [auth V]
54Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9J,
U [auth W]
64Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00130 (Bos taurus)
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UniProt GroupP00130
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10K,
V [auth X]
49Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07552 (Bos taurus)
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
CA [auth Q],
Y [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth P],
BA [auth P],
W [auth C],
X [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
DA [auth R],
Z [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0.0
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland176154
Wellcome TrustUnited KingdomWT110068/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-04-30
    Changes: Data collection, Database references