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- PDB-9f5z: Structure of the Chlamydomonas reinhardtii respiratory complex II... -

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Basic information

Entry
Database: PDB / ID: 9f5z
TitleStructure of the Chlamydomonas reinhardtii respiratory complex III from respiratory supercomplex
Components
  • (Cytochrome b-c1 complex subunit ...) x 3
  • (Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit ...) x 2
  • Alpha-MPP
  • Complex III subunit 9
  • Cytochrome b
  • Cytochrome c1
  • MPP-Beta
KeywordsMEMBRANE PROTEIN / Mitochondria / respiratory complex / respiration / alga
Function / homology
Function and homology information


quinol-cytochrome-c reductase / mitochondrial processing peptidase / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / metallopeptidase activity / electron transfer activity ...quinol-cytochrome-c reductase / mitochondrial processing peptidase / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / metallopeptidase activity / electron transfer activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 ...Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / 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 / 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 / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 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
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / HEME C / Chem-PC7 / PHOSPHATIDYLETHANOLAMINE / Chem-UQ5 / Cytochrome b-c1 complex subunit 7 / Uncharacterized protein / Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10 / mitochondrial processing peptidase ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / HEME C / Chem-PC7 / PHOSPHATIDYLETHANOLAMINE / Chem-UQ5 / Cytochrome b-c1 complex subunit 7 / Uncharacterized protein / Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10 / mitochondrial processing peptidase / Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8 / Cytochrome b-c1 complex subunit 6 / Complex III subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome c1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsWaltz, F. / Righetto, R. / Kotecha, A. / Engel, B.D.
Funding support Germany, Switzerland, 2items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Swiss National Science Foundation210561 Switzerland
CitationJournal: Science / Year: 2025
Title: In-cell architecture of the mitochondrial respiratory chain.
Authors: Florent Waltz / Ricardo D Righetto / Lorenz Lamm / Thalia Salinas-Giegé / Ron Kelley / Xianjun Zhang / Martin Obr / Sagar Khavnekar / Abhay Kotecha / Benjamin D Engel /
Abstract: Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, ...Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (Å) resolution structure showing binding of electron carrier cytochrome . Combined with single-particle cryo-electron microscopy at 2.4-Å resolution, we model how the respiratory complexes organize inside native mitochondria.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: Cytochrome b
1B: Cytochrome b
1C: Cytochrome b-c1 complex subunit Rieske, mitochondrial
1D: Cytochrome b-c1 complex subunit Rieske, mitochondrial
1E: Cytochrome c1
1F: Cytochrome c1
1G: Complex III subunit 9
1H: Complex III subunit 9
1I: Cytochrome b-c1 complex subunit 6
1J: Cytochrome b-c1 complex subunit 6
1K: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8
1L: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8
1M: MPP-Beta
1N: MPP-Beta
1O: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10
1P: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10
1Q: Alpha-MPP
1R: Cytochrome b-c1 complex subunit 7
1S: Alpha-MPP
1T: Cytochrome b-c1 complex subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,13651
Polymers507,56220
Non-polymers25,57431
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 10 molecules 1A1B1E1F1G1H1M1N1Q1S

#1: Protein Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42356.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P23662
#3: Protein Cytochrome c1


Mass: 33868.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9FQ96, quinol-cytochrome-c reductase
#4: Protein Complex III subunit 9


Mass: 7040.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JC51
#7: Protein MPP-Beta


Mass: 55121.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J5P7
#9: Protein Alpha-MPP


Mass: 49640.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IKI9

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Cytochrome b-c1 complex subunit ... , 3 types, 6 molecules 1C1D1I1J1R1T

#2: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 28545.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8HEB4, quinol-cytochrome-c reductase
#5: Protein Cytochrome b-c1 complex subunit 6


Mass: 7991.032 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J8N9
#10: Protein Cytochrome b-c1 complex subunit 7


Mass: 14062.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HX89

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Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit ... , 2 types, 4 molecules 1K1L1O1P

#6: Protein Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8


Mass: 8678.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J7I9, quinol-cytochrome-c reductase
#8: Protein Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10


Mass: 6476.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J4K5, quinol-cytochrome-c reductase

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Non-polymers , 8 types, 569 molecules

#11: Chemical
ChemComp-UQ5 / 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE


Mass: 522.758 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H50O4
#12: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#13: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#14: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C39H77O8P
#15: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#16: Chemical ChemComp-PC7 / (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 1-PALMITOYL-2-STEAROYL-PC


Mass: 763.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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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

ComponentName: Chlamydomonas reinhardtii respirasome / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83443 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006139259
ELECTRON MICROSCOPYf_angle_d0.865188735
ELECTRON MICROSCOPYf_dihedral_angle_d10.39120602
ELECTRON MICROSCOPYf_chiral_restr0.05320306
ELECTRON MICROSCOPYf_plane_restr0.00723689

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