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- PDB-6q9e: Complex III2 focused refinement from Ovine respiratory supercompl... -

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Basic information

Entry
Database: PDB / ID: 6q9e
TitleComplex III2 focused refinement from Ovine respiratory supercomplex I+III2
Components
  • (Cytochrome b-c1 complex subunit ...) x 4
  • (Ubiquinol-cytochrome c ...) x 4
  • Cytochrome b
  • Cytochrome c1
KeywordsELECTRON TRANSPORT / complex III / cellular respiration / mitochondria
Function / homology
Function and homology information


: / : / : / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / membrane => GO:0016020 / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding ...: / : / : / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / membrane => GO:0016020 / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / ubiquitin protein ligase binding / proteolysis / nucleoplasm / metal ion binding
Similarity search - Function
Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit ...Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 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 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / UBIQUINONE-10 / Cytochrome b-c1 complex subunit 6 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / UBIQUINONE-10 / Cytochrome b-c1 complex subunit 6 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Complex III subunit 9 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 6 / cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLetts, J.A. / Sazanov, L.A.
Funding support Austria, 1items
OrganizationGrant numberCountry
European Research Council701309 Austria
CitationJournal: Mol Cell / Year: 2019
Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk.
Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov /
Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

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Assembly

Deposited unit
a1: Ubiquinol-cytochrome c reductase core protein 1
a2: Ubiquinol-cytochrome c reductase core protein 2
b1: Cytochrome b
c1: Cytochrome c1
f1: Cytochrome b-c1 complex subunit Rieske, mitochondrial
d1: Cytochrome b-c1 complex subunit 7
q1: Ubiquinol-cytochrome c reductase complex III subunit VII
h1: Cytochrome b-c1 complex subunit 6
x1: Cytochrome b-c1 complex subunit Rieske, mitochondrial
i1: Ubiquinol-cytochrome c reductase, complex III subunit X
a3: Ubiquinol-cytochrome c reductase core protein 1
a4: Ubiquinol-cytochrome c reductase core protein 2
b2: Cytochrome b
c2: Cytochrome c1
f2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
d2: Cytochrome b-c1 complex subunit 7
q2: Ubiquinol-cytochrome c reductase complex III subunit VII
h2: Cytochrome b-c1 complex subunit 6
x2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
i2: Ubiquinol-cytochrome c reductase, complex III subunit X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)477,54540
Polymers460,58820
Non-polymers16,95720
Water00
1


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

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Components

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Ubiquinol-cytochrome c ... , 4 types, 8 molecules a1a3a2a4q1q2i1i2

#1: Protein Ubiquinol-cytochrome c reductase core protein 1


Mass: 49385.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5Q5G6
#2: Protein Ubiquinol-cytochrome c reductase core protein 2


Mass: 46655.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5Q0F9
#7: Protein Ubiquinol-cytochrome c reductase complex III subunit VII


Mass: 9606.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PUP9
#10: Protein Ubiquinol-cytochrome c reductase, complex III subunit X


Mass: 7310.372 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5P6B2

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Protein , 2 types, 4 molecules b1b2c1c2

#3: 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: 42877.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: P24959
#4: Protein Cytochrome c1


Mass: 27322.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5Q0A9

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Cytochrome b-c1 complex subunit ... , 4 types, 8 molecules f1f2d1d2h1h2x1x2

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


Mass: 21654.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5P2X9, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 7


Mass: 13432.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5P642
#8: Protein Cytochrome b-c1 complex subunit 6


Mass: 9223.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PZC9, UniProt: B9VH04*PLUS
#9: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 2826.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Modeled as poly-alanine due to poor density. / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac

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Non-polymers , 6 types, 20 molecules

#11: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#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.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#14: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C59H90O4
#15: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#16: 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 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: Ovine mitochondrial SC I+III2 / Type: COMPLEX
Details: Complex III2 focused refinement from ovine respiratory SC I+III2
Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)Organism: Ovis aries (sheep) / Cellular location: Mitochondrial inner membrane / Organ: Heart / Organelle: Mitochondria / Tissue: Cardiac
Buffer solutionpH: 7.4 / Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
Buffer component
IDConc.NameFormulaBuffer-ID
10.25 Msodium chlorideNaCl1
20.02 MHEPES1
30.02 %Brij-351
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 95 % / Chamber temperature: 277 K
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing

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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: OTHER
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 51 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1854
Image scansMovie frames/image: 34

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.13-2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 400000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102314 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 1PPJ

1ppj


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

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