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- PDB-6f0k: Alternative complex III -

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Basic information

Entry
Database: PDB / ID: 6f0k
TitleAlternative complex III
Components
  • ActD
  • ActF
  • ActHAdrenocorticotropic hormone
  • Cytochrome c family protein
  • Fe-S-cluster-containing hydrogenase
  • Polysulphide reductase NrfD
  • Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit
KeywordsMEMBRANE PROTEIN / electron transfer / quinol oxidation / respiratory chain
Function / homology
Function and homology information


electron transfer activity / membrane => GO:0016020 / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Menaquinone reductase, multiheme cytochrome c subunit / NrfD family / Alternative complex III, ActD subunit / MoCo/4Fe-4S cofactor protein extended Tat translocation domain / Polysulphide reductase, NrfD / Alternative complex III, ActD subunit / : / Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Multiheme cytochrome c family profile. ...Menaquinone reductase, multiheme cytochrome c subunit / NrfD family / Alternative complex III, ActD subunit / MoCo/4Fe-4S cofactor protein extended Tat translocation domain / Polysulphide reductase, NrfD / Alternative complex III, ActD subunit / : / Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Multiheme cytochrome c family profile. / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
FE3-S4 CLUSTER / HEME C / IRON/SULFUR CLUSTER / Cytochrome c family protein / Fe-S-cluster-containing hydrogenase / Polysulphide reductase NrfD / Uncharacterized protein / Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsSousa, J.S. / Calisto, F. / Mills, D.J. / Pereira, M.M. / Vonck, J. / Kuehlbrandt, W.
Funding support Portugal, Germany, 2items
OrganizationGrant numberCountry
Fundacao para a ciencia e tecnologiaIF/01507/2015 Portugal
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for energy transduction by respiratory alternative complex III.
Authors: Joana S Sousa / Filipa Calisto / Julian D Langer / Deryck J Mills / Patrícia N Refojo / Miguel Teixeira / Werner Kühlbrandt / Janet Vonck / Manuela M Pereira /
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 ...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.
History
DepositionNov 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-4165
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c family protein
B: Fe-S-cluster-containing hydrogenase
C: Polysulphide reductase NrfD
D: ActD
E: Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit
F: ActF
H: ActH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,83517
Polymers310,7737
Non-polymers5,06210
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The chains were identified in the EM map
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area46050 Å2
ΔGint-435 kcal/mol
Surface area87860 Å2
MethodPISA

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Components

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Protein , 7 types, 7 molecules ABCDEFH

#1: Protein Cytochrome c family protein


Mass: 24245.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / References: UniProt: D0MDD4
#2: Protein Fe-S-cluster-containing hydrogenase


Mass: 115382.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / References: UniProt: D0MDD5
#3: Protein Polysulphide reductase NrfD


Mass: 55256.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / References: UniProt: D0MDD6
#4: Protein ActD


Mass: 23796.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / References: UniProt: D0MDD7
#5: Protein Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit


Mass: 23336.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / References: UniProt: D0MDD8
#6: Protein ActF


Mass: 48536.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / References: UniProt: D0MDD9
#7: Protein ActH / Adrenocorticotropic hormone


Mass: 20219.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / References: UniProt: D0MKF0

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Non-polymers , 3 types, 10 molecules

#8: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#9: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#10: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Alternative complex III / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 300 kDa/nm / Experimental value: NO
Source (natural)Organism: Rhodothermus marinus (bacteria) / Strain: PRQ-62B
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 72 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52386 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00940763
ELECTRON MICROSCOPYf_angle_d1.05773504
ELECTRON MICROSCOPYf_dihedral_angle_d12.98816344
ELECTRON MICROSCOPYf_chiral_restr0.0853049
ELECTRON MICROSCOPYf_plane_restr0.0065986

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