[English] 日本語
Yorodumi
- PDB-6xkw: R. capsulatus CIII2CIV bipartite super-complex (SC-2A) with CcoH/cy -

+
Open data


ID or keywords:

Loading...

-
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 / plasma membrane respiratory chain complex IV / respiratory chain complex III / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / photosynthesis ...cytochrome-c oxidase / plasma membrane respiratory chain complex IV / respiratory chain complex III / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / photosynthesis / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / intracellular membrane-bounded organelle / heme binding / membrane / metal ion binding / plasma membrane / cytoplasm
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 oxidase, cbb3-type, subunit III / Cytochrome c, class IA/ IB / Cytochrome b / : / : / 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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Cytochrome c / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-22227
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
1


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

-
Components

-
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

-
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

-
Non-polymers , 3 types, 14 molecules

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


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


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


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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
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

-
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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more