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Entry
Database: PDB / ID: 8b6g
TitleCryo-EM structure of succinate dehydrogenase complex (complex-II) in respiratory supercomplex of Tetrahymena thermophila
Components
  • (Succinate dehydrogenase ...) x 2
  • (Transmembrane protein, ...) x 5
  • Cytochrome b-c1 complex subunit 8
  • DUF4885 domain-containing protein
  • Diphthamide synthesis protein
  • NmrA domain-containing protein
  • SDHD
  • SDHTT11
  • SDHTT3
  • Transposase
KeywordsELECTRON TRANSPORT / Ciliate / Mitochondrial / Complex-II / Supercomplex
Function / homology
Function and homology information


: / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / 3 iron, 4 sulfur cluster binding / tricarboxylic acid cycle / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / mitochondrial inner membrane / electron transfer activity / membrane
Similarity search - Function
Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal ...Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HEME C / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Ubiquinone-8 / Diphthamide synthesis protein ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HEME C / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Ubiquinone-8 / Diphthamide synthesis protein / succinate dehydrogenase / Uncharacterized protein / Transmembrane protein, putative / Uncharacterized protein / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Transmembrane protein / Transmembrane protein, putative / Transmembrane protein, putative / Transmembrane protein, putative / NmrA-like domain-containing protein / Uncharacterized protein / Transmembrane protein, putative
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMuhleip, A. / Kock Flygaard, R. / Baradaran, 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
CH: Diphthamide synthesis protein
CM: Transmembrane protein, putative
CL: Transposase
CA: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
CI: DUF4885 domain-containing protein
CB: Succinate dehydrogenase (quinone)
CF: Transmembrane protein, putative
CG: SDHTT3
CK: Transmembrane protein, putative
CE: NmrA domain-containing protein
CJ: Transmembrane protein, putative
CN: Transmembrane protein, putative
CC: Cytochrome b-c1 complex subunit 8
CO: SDHTT11
CD: SDHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,75234
Polymers305,43415
Non-polymers16,31719
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area91310 Å2
ΔGint-675 kcal/mol
Surface area91850 Å2
MethodPISA

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Components

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Protein , 6 types, 6 molecules CHCLCICGCECC

#1: Protein Diphthamide synthesis protein


Mass: 22894.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: I7LX66
#3: Protein Transposase /


Mass: 11027.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: W7XBF5
#5: Protein DUF4885 domain-containing protein


Mass: 12979.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q22YL0
#8: Protein SDHTT3


Mass: 23627.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: I7MEX7
#10: Protein NmrA domain-containing protein


Mass: 36376.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q24I09
#13: Protein Cytochrome b-c1 complex subunit 8


Mass: 7036.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q23RH8

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Transmembrane protein, ... , 5 types, 5 molecules CMCFCKCJCN

#2: Protein Transmembrane protein, putative / Transmembrane protein


Mass: 9168.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q22HD6
#7: Protein Transmembrane protein, putative / Transmembrane protein


Mass: 35124.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q248F8
#9: Protein Transmembrane protein, putative / Transmembrane protein


Mass: 11188.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q24CW6
#11: Protein Transmembrane protein, putative / Transmembrane protein


Mass: 11957.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q23S01
#12: Protein Transmembrane protein, putative / Transmembrane protein


Mass: 7244.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: W7XF00

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Succinate dehydrogenase ... , 2 types, 2 molecules CACB

#4: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial


Mass: 70082.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q23DI3, succinate dehydrogenase
#6: Protein Succinate dehydrogenase (quinone) / Iron-sulfur subunit of complex II


Mass: 36002.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: I7M403, succinate dehydrogenase

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Protein/peptide , 2 types, 2 molecules COCD

#14: Protein/peptide SDHTT11


Mass: 5158.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#15: Protein/peptide SDHD


Mass: 5566.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)

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Non-polymers , 10 types, 19 molecules

#16: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#17: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#18: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#19: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#23: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#25: 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.: 1 / Source method: obtained synthetically / Formula: C49H74O4 / 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: Succinate dehydrogenase complex (complex-II) / Type: COMPLEX
Details: Complex-II of the mitochondrial respiratory chain in Tetrahymena thermophila
Entity ID: #1-#15 / Source: NATURAL
Molecular weightValue: 0.305 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 FIELDBright-field microscopy / 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: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138746 / Symmetry type: POINT

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