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- PDB-6xkw: R. capsulatus CIII2CIV bipartite super-complex (SC-2A) with CcoH/cy -

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Basic information

Entry
Database: PDB / ID: 6xkw
TitleR. capsulatus CIII2CIV bipartite super-complex (SC-2A) with CcoH/cy
Components
  • (Cytochrome c oxidase, Cbb3-type, subunit ...) x 2
  • Cbb3-type cytochrome c oxidase subunit CcoP
  • Cytochrome b
  • Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH
  • Cytochrome c-type cyt cy
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsTRANSLOCASE/Oxidoreductase / cytochrome bc1 / cbb3-COX / Complex III / Complex IV / OXIDOREDUCTASE / TRANSLOCASE-Oxidoreductase complex
Function / homology
Function and homology information


cytochrome-c oxidase / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / photosynthesis / proton transmembrane transport ...cytochrome-c oxidase / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / photosynthesis / proton transmembrane transport / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Nitrogen fixation protein FixH / Nitrogen fixation protein FixH, Proteobacterial / FixH / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP ...Nitrogen fixation protein FixH / Nitrogen fixation protein FixH, Proteobacterial / FixH / Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / : / Cytochrome c, class IA/ IB / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / 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 / Cytochrome c / 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
COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME C / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1 / cytochrome-c oxidase / Cytochrome c oxidase, Cbb3-type, subunit II / Cbb3-type cytochrome c oxidase subunit CcoP / Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH / Cytochrome c-type cyt cy
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 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, Israel, 8items
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
Israel Science Foundation1466/18 Israel
United States - Israel Binational Science Foundation (BSF)2016070 Israel
Israel Ministry of Science and Technology80802 Israel
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 27, 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 1.2Oct 23, 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

Movie
  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-22227
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Assembly

Deposited unit
n: Cytochrome c oxidase, Cbb3-type, subunit I
o: Cytochrome c oxidase, Cbb3-type, subunit II
p: Cbb3-type cytochrome c oxidase subunit CcoP
h: Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH
Y: Cytochrome c-type cyt cy
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)362,30825
Polymers355,08911
Non-polymers7,21914
Water00
1


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

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Components

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Cytochrome c oxidase, Cbb3-type, subunit ... , 2 types, 2 molecules no

#1: Protein Cytochrome c oxidase, Cbb3-type, subunit I


Mass: 58975.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / References: UniProt: D5ARP4, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase, Cbb3-type, subunit II


Mass: 26998.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / References: UniProt: D5ARP5, cytochrome-c oxidase

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Protein , 6 types, 9 molecules phYERCPDQ

#3: Protein Cbb3-type cytochrome c oxidase subunit CcoP / Cbb3-Cox subunit CcoP / C-type cytochrome CcoP / Cyt c(P) / Cytochrome c oxidase subunit III


Mass: 31739.598 Da / Num. of mol.: 1
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: ccoP, RCAP_rcc01160 / Plasmid: pYO76 / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / Strain (production host): YO12 / References: UniProt: D5ARP7
#4: Protein Cytochrome c oxidase, Cbb3-type, biogenesis protein CcoH


Mass: 16285.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / References: UniProt: D5ARP9
#5: Protein Cytochrome c-type cyt cy


Mass: 20681.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / References: UniProt: Q05389
#6: 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
#7: 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
#8: 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

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Non-polymers , 3 types, 14 molecules

#9: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#10: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#11: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

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Details

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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1CIII2CIV bipartite super-complex (SC-2A) with CcoH/cyCOMPLEXsuper-complex assembly with genetic fusion between cyt c1 and CcoP, CcoH copurified with the complex, cyt cy was added to the sample#1-#80RECOMBINANT
2CIII2COMPLEXubiquinol:cytochrome c reductase (cytochrome bc1, CIII2) portion of the super-complex#1-#31RECOMBINANT
3CIVCOMPLEXcbb3-type cytochrome c oxidase (CIV) portion of the super-complex#4-#61RECOMBINANT
4CcoH/cyCOMPLEX2 additional transmembrane helices at the interface of CIII2 and CIV which were identified as the single TMHs of CcoH and cyt cy#7-#81NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.45 MDaNO
21NO
31NO
41NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rhodobacter capsulatus SB 1003 (bacteria)272942
32Rhodobacter capsulatus SB 1003 (bacteria)272942
43Rhodobacter capsulatus SB 1003 (bacteria)272942
54Rhodobacter capsulatus SB 1003 (bacteria)272942
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
21Rhodobacter capsulatus SB 1003 (bacteria)272942YO12pYO76
32Rhodobacter capsulatus SB 1003 (bacteria)272942YO12pYO76
43Rhodobacter capsulatus SB 1003 (bacteria)272942YO12pYO76
54Rhodobacter capsulatus SB 1003 (bacteria)272942YO12pYO76
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: 716907
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14978 / Symmetry type: POINT
Atomic model buildingB value: 87 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 6XI0

6xi0


Accession code: 6XI0 / Source name: PDB / Type: experimental model

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