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- PDB-8b6j: Cryo-EM structure of cytochrome bc1 complex (complex-III) from re... -

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Basic information

Entry
Database: PDB / ID: 8b6j
TitleCryo-EM structure of cytochrome bc1 complex (complex-III) from respiratory supercomplex of Tetrahymena thermophila
Components
  • (Transmembrane protein, ...) x 3
  • Apocytochrome b
  • Cytochrome protein c1
  • M16 family peptidase, putative
  • Peptidase M16 inactive domain protein
  • Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit
  • UQCRTT1
  • UQCRTT2
  • UQCRTT3/UP1
  • Ubiquinol-cytochrome C reductase hinge protein
KeywordsELECTRON TRANSPORT / Ciliate / mitochondrial / cytochrome bc1 / supercomplex
Function / homology
Function and homology information


quinol-cytochrome-c reductase / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity ...quinol-cytochrome-c reductase / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / electron transfer activity / heme binding / mitochondrion / membrane / metal ion binding / plasma membrane
Similarity search - Function
Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1 / Cytochrome C1 family / 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 ...Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1 / Cytochrome C1 family / 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] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Ubiquinone-8 / Transmembrane protein, putative / Transmembrane protein, putative / Peptidase M16 inactive domain protein ...CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Ubiquinone-8 / Transmembrane protein, putative / Transmembrane protein, putative / Peptidase M16 inactive domain protein / Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit / M16 family peptidase, putative / Transmembrane protein, putative / Uncharacterized protein / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome protein c1 / Apocytochrome b
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMuhleip, A. / Kock Flygaard, R. / Amunts, A.
Funding support Sweden, European Union, 4items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
Cancerfonden2017/1041 Sweden
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
Citation
Journal: Nature / Year: 2023
Title: Structural basis of mitochondrial membrane bending by the I-II-III-IV supercomplex.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Rozbeh Baradaran / Outi Haapanen / Thomas Gruhl / Victor Tobiasson / Amandine Maréchal / Vivek Sharma / Alexey Amunts /
Abstract: Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes ...Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III-IV supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex
Authors: Muhleip, A. / Flygaard, R.K. / Haapanen, O. / Baradaran, R. / Gruhl, T. / Tobiasson, V. / Marechal, A. / Sharma, V. / Amunts, A.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase M16 inactive domain protein
B: M16 family peptidase, putative
C: Apocytochrome b
D: Cytochrome protein c1
E: Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit
F: Ubiquinol-cytochrome C reductase hinge protein
G: UQCRTT1
H: Transmembrane protein, putative
I: Transmembrane protein, putative
J: UQCRTT3/UP1
K: Transmembrane protein, putative
a: Peptidase M16 inactive domain protein
b: M16 family peptidase, putative
c: Apocytochrome b
d: Cytochrome protein c1
e: Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit
f: Ubiquinol-cytochrome C reductase hinge protein
g: UQCRTT1
h: Transmembrane protein, putative
i: Transmembrane protein, putative
j: UQCRTT3/UP1
k: Transmembrane protein, putative
l: UQCRTT2
L: UQCRTT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)695,46567
Polymers653,92824
Non-polymers41,53743
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 , 8 types, 16 molecules AaBbCcDdEeFfGgJj

#1: Protein Peptidase M16 inactive domain protein


Mass: 58023.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MGU2
#2: Protein M16 family peptidase, putative


Mass: 53030.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MJ25
#3: Protein Apocytochrome b


Mass: 50635.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q950Z1
#4: Protein Cytochrome protein c1


Mass: 37616.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q24IM5
#5: Protein Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunit


Mass: 30696.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MIC7
#6: Protein Ubiquinol-cytochrome C reductase hinge protein


Mass: 9885.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23K66
#7: Protein UQCRTT1


Mass: 39193.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23F81
#10: Protein UQCRTT3/UP1


Mass: 5634.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)

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Transmembrane protein, ... , 3 types, 6 molecules HhIiKk

#8: Protein Transmembrane protein, putative


Mass: 15677.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M484
#9: Protein Transmembrane protein, putative


Mass: 14262.554 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MM45
#11: Protein Transmembrane protein, putative


Mass: 7455.741 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MFL6

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Protein/peptide , 1 types, 2 molecules lL

#12: Protein/peptide UQCRTT2


Mass: 4850.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)

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Non-polymers , 7 types, 43 molecules

#13: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#14: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#15: 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.: 15 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#16: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#18: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Dimeric cytochrome bc1 complex (complex-III2) / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 0.64 MDa / Experimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Organelle: Mitochondrion
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 defocus max: 2600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 25.66 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138746 / Symmetry type: POINT

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