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- PDB-8iog: Cryo-EM structure of porcine bc1 complex in isolated state -

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Basic information

Entry
Database: PDB / ID: 8iog
TitleCryo-EM structure of porcine bc1 complex in isolated state
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • Complex III subunit 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsELECTRON TRANSPORT / Complex / mitochondria
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / Respiratory electron transport / Mitochondrial protein degradation / : / quinol-cytochrome-c reductase ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / thalamus development / Respiratory electron transport / Mitochondrial protein degradation / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / : / hippocampus development / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / 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 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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 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 / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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
CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 2, mitochondrial ...CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 6 / Cytochrome b / Complex III subunit 9
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsWang, Y.X. / Dong, J.Q. / Yang, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of porcine bc1 complex in isolated state
Authors: Wang, Y.X. / Dong, J.Q. / Yang, G.F.
History
DepositionMar 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b
B: Cytochrome c1, heme protein, mitochondrial
C: Cytochrome b-c1 complex subunit Rieske, mitochondrial
D: Cytochrome b-c1 complex subunit 1, mitochondrial
E: Cytochrome b-c1 complex subunit 2, mitochondrial
F: Cytochrome b-c1 complex subunit 6
G: Cytochrome b-c1 complex subunit 7
H: Cytochrome b-c1 complex subunit 8
I: Complex III subunit 9
J: Cytochrome b-c1 complex subunit 10
K: Cytochrome b-c1 complex subunit Rieske, mitochondrial
a: Cytochrome b
b: Cytochrome c1, heme protein, mitochondrial
c: Cytochrome b-c1 complex subunit Rieske, mitochondrial
d: Cytochrome b-c1 complex subunit 1, mitochondrial
e: Cytochrome b-c1 complex subunit 2, mitochondrial
f: Cytochrome b-c1 complex subunit 6
g: Cytochrome b-c1 complex subunit 7
h: Cytochrome b-c1 complex subunit 8
i: Complex III subunit 9
j: Cytochrome b-c1 complex subunit 10
k: Cytochrome b-c1 complex subunit Rieske, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,99935
Polymers513,78422
Non-polymers9,21513
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 6 molecules AaBbIi

#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: 42840.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MT-CYB, COB, CYTB, MTCYB / Production host: Sus scrofa (pig) / References: UniProt: P24964
#2: Protein Cytochrome c1, heme protein, mitochondrial


Mass: 35488.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: LOC100525869 / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1UNI7
#9: Protein Complex III subunit 9


Mass: 7412.530 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: UQCR10 / Production host: Sus scrofa (pig) / References: UniProt: Q2EN79

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Cytochrome b-c1 complex subunit ... , 8 types, 16 molecules CcDdEeFfGgHhJjKk

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


Mass: 21610.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: LOC100522678 / Production host: Sus scrofa (pig)
References: UniProt: A0A4X1TWD8, quinol-cytochrome-c reductase
#4: Protein Cytochrome b-c1 complex subunit 1, mitochondrial


Mass: 52756.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: LOC100156879 / Production host: Sus scrofa (pig) / References: UniProt: A0A8D0PK14
#5: Protein Cytochrome b-c1 complex subunit 2, mitochondrial


Mass: 48264.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1V0F2
#6: Protein Cytochrome b-c1 complex subunit 6


Mass: 10685.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: UQCRH, LOC100524873 / Production host: Sus scrofa (pig) / References: UniProt: F1S3W0
#7: Protein Cytochrome b-c1 complex subunit 7


Mass: 13587.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: UQCRB / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1U2M7
#8: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8


Mass: 9784.339 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: UQCRQ, LOC100524308 / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1UYT9
#10: Protein Cytochrome b-c1 complex subunit 10


Mass: 6560.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: LOC100524239 / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1VTU3
#11: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 7900.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Author stated: Chain C/c and Chain K/k are truly from one polypeptide, and the polypeptide will be cleaved into two chains upon maturation.
Source: (gene. exp.) Sus scrofa (pig) / Gene: LOC100522678 / Production host: Sus scrofa (pig)
References: UniProt: A0A4X1TWD8, quinol-cytochrome-c reductase

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Non-polymers , 5 types, 13 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#13: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#14: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#16: 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.: 2 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM

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Details

Has ligand of interestN

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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: porcine Cytochrome bc1 complex / Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.4 / Details: PBS, 0.1% DDM
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 49.21 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 701

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 191014
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98300 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 5GUP

5gup


Accession code: 5GUP / Source name: PDB / Type: experimental model

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