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- PDB-6xi0: R. capsulatus cyt bc1 (CIII2) at 3.3A -

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Basic information

Entry
Database: PDB / ID: 6xi0
TitleR. capsulatus cyt bc1 (CIII2) at 3.3A
Components
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / cytochrome bc1 membrane protein complex ubiquinone:cytochrome c oxidoreductase Complex III
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / : / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSteimle, S. / Van Eeuwen, T. / Ozturk, Y. / Kim, H.J. / Braitbard, M. / Selamoglu, N. / Garcia, B.A. / Schneidman-Duhovny, D. / Murakami, K. / Daldal, F.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM38237 United States
Department of Energy (DOE, United States)DE-FG02-91ER20052 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD023592 United States
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structures of engineered active bc-cbb type CIIICIV super-complexes and electronic communication between the complexes.
Authors: Stefan Steimle / Trevor van Eeuwen / Yavuz Ozturk / Hee Jong Kim / Merav Braitbard / Nur Selamoglu / Benjamin A Garcia / Dina Schneidman-Duhovny / Kenji Murakami / Fevzi Daldal /
Abstract: Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc (Complex ...Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc (Complex III, CIII), and may have specific cbb-type cyt c oxidases (Complex IV, CIV) instead of the canonical aa-type CIV. Electron transfer between these complexes is mediated by soluble (c) and membrane-anchored (c) cyts. Here, we report the structure of an engineered bc-cbb type SC (CIIICIV, 5.2 Å resolution) and three conformers of native CIII (3.3 Å resolution). The SC is active in vivo and in vitro, contains all catalytic subunits and cofactors, and two extra transmembrane helices attributed to cyt c and the assembly factor CcoH. The cyt c is integral to SC, its cyt domain is mobile and it conveys electrons to CIV differently than cyt c. The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria.
History
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-22189
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
E: Ubiquinol-cytochrome c reductase iron-sulfur subunit
C: Cytochrome b
D: Cytochrome c1
P: Cytochrome b
Q: Cytochrome c1
R: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,47114
Polymers200,4086
Non-polymers4,0638
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 20465.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / Gene: petA, fbcF, RCAP_rcc02768 / Plasmid: pYO76 / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / Strain (production host): YO12 / References: UniProt: D5ANZ2, quinol-cytochrome-c reductase
#2: Protein Cytochrome b


Mass: 49386.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / Gene: petB, cytB, RCAP_rcc02769 / Plasmid: pYO76 / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / Strain (production host): YO12 / References: UniProt: D5ANZ3
#3: Protein Cytochrome c1


Mass: 30352.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / Gene: petC, RCAP_rcc02770 / Plasmid: pYO76 / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / Strain (production host): YO12 / References: UniProt: D5ANZ4
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has ligand of interestN
Has protein modificationY

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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: homodimer of ubiquinol:cytochrome c reductase (complex III or cyt bc1 complex)
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Source (recombinant)Organism: Rhodobacter capsulatus SB 1003 (bacteria) / Strain: YO12 / Plasmid: pYO76
Buffer solutionpH: 7.4
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4RELION3CTF correctionCTFFIND 4.1 was used
7UCSF Chimera1.14model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 267467
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37997 / Symmetry type: POINT
Atomic model buildingB value: 33 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 1ZRT

1zrt


Accession code: 1ZRT / Source name: PDB / Type: experimental model

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