6F0K | pdb_00006f0k

Alternative complex III


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6F0K

This is version 2.3 of the entry. See complete history

Literature

Structural basis for energy transduction by respiratory alternative complex III.

Sousa, J.S.Calisto, F.Langer, J.D.Mills, D.J.Refojo, P.N.Teixeira, M.Kuhlbrandt, W.Vonck, J.Pereira, M.M.

(2018) Nat Commun 9: 1728-1728

  • DOI: https://doi.org/10.1038/s41467-018-04141-8
  • Primary Citation Related Structures: 
    6F0K

  • PubMed Abstract: 

    Electron transfer in respiratory chains generates the electrochemical potential that serves as energy source for the cell. Prokaryotes can use a wide range of electron donors and acceptors and may have alternative complexes performing the same catalytic reactions as the mitochondrial complexes. This is the case for the alternative complex III (ACIII), a quinol:cytochrome c/HiPIP oxidoreductase. In order to understand the catalytic mechanism of this respiratory enzyme, we determined the structure of ACIII from Rhodothermus marinus at 3.9 Å resolution by single-particle cryo-electron microscopy. ACIII presents a so-far unique structure, for which we establish the arrangement of the cofactors (four iron-sulfur clusters and six c-type hemes) and propose the location of the quinol-binding site and the presence of two putative proton pathways in the membrane. Altogether, this structure provides insights into a mechanism for energy transduction and introduces ACIII as a redox-driven proton pump.


  • Organizational Affiliation
    • Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany.

Macromolecule Content 

  • Total Structure Weight: 315.84 kDa 
  • Atom Count: 20,291 
  • Modeled Residue Count: 2,504 
  • Deposited Residue Count: 2,759 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c family protein211Rhodothermus marinus DSM 4252Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0MDD4 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MDD4 
Go to UniProtKB:  D0MDD4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0MDD4
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fe-S-cluster-containing hydrogenase1,039Rhodothermus marinus DSM 4252Mutation(s): 0 
UniProt
Find proteins for D0MDD5 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MDD5 
Go to UniProtKB:  D0MDD5
Entity Groups
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UniProt GroupD0MDD5
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Polysulphide reductase NrfD484Rhodothermus marinus DSM 4252Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0MDD6 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MDD6 
Go to UniProtKB:  D0MDD6
Entity Groups
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UniProt GroupD0MDD6
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ActD217Rhodothermus marinus DSM 4252Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0MDD7 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MDD7 
Go to UniProtKB:  D0MDD7
Entity Groups
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UniProt GroupD0MDD7
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit209Rhodothermus marinus DSM 4252Mutation(s): 0 
UniProt
Find proteins for D0MDD8 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MDD8 
Go to UniProtKB:  D0MDD8
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UniProt GroupD0MDD8
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ActF417Rhodothermus marinus DSM 4252Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0MDD9 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MDD9 
Go to UniProtKB:  D0MDD9
Entity Groups
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UniProt GroupD0MDD9
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
ActHG [auth H]182Rhodothermus marinus DSM 4252Mutation(s): 0 
UniProt
Find proteins for D0MKF0 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MKF0 
Go to UniProtKB:  D0MKF0
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UniProt GroupD0MKF0
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC

Query on HEC



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
Q [auth E]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
N [auth B],
O [auth B],
P [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S



Download:Ideal Coordinates CCD File
M [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a ciencia e tecnologiaPortugalIF/01507/2015
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 2.0: 2018-12-19
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2019-12-11
    Changes: Other
  • Version 2.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.3: 2025-07-02
    Changes: Data collection