[English] 日本語
Yorodumi
- PDB-8gs8: cryo-EM structure of the human respiratory complex II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gs8
Titlecryo-EM structure of the human respiratory complex II
Components
  • (Succinate dehydrogenase [ubiquinone] ...) x 3
  • Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
KeywordsOXIDOREDUCTASE / succinate dehydrogenase / electron transport chain / human mitochondria / oxidative phosphorylation
Function / homology
Function and homology information


regulation of catecholamine secretion / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / succinate metabolic process / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport ...regulation of catecholamine secretion / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / succinate metabolic process / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport / mitochondrial envelope / 3 iron, 4 sulfur cluster binding / ubiquinone binding / proton motive force-driven mitochondrial ATP synthesis / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / nervous system development / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / cellular response to hypoxia / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / heme binding / nucleolus / mitochondrion / nucleoplasm / metal ion binding / membrane / plasma membrane
Similarity search - Function
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit ...Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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 / FAD binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 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
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-PEV / IRON/SULFUR CLUSTER / UBIQUINONE-1 / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsDu, Z. / Zhou, X. / Lai, Y. / Xu, J. / Zhang, Y. / Zhou, S. / Liu, F. / Gao, Y. / Gong, H. / Rao, Z.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020200 China
National Natural Science Foundation of China (NSFC)81520108019, 813300237,32100976,82222042 China
Chinese Academy of Sciences2017YFC0840300,2020YFA0707500 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure of the human respiratory complex II.
Authors: Zhanqiang Du / Xiaoting Zhou / Yuezheng Lai / Jinxu Xu / Yuying Zhang / Shan Zhou / Ziyan Feng / Long Yu / Yanting Tang / Weiwei Wang / Lu Yu / Changlin Tian / Ting Ran / Hongming Chen / ...Authors: Zhanqiang Du / Xiaoting Zhou / Yuezheng Lai / Jinxu Xu / Yuying Zhang / Shan Zhou / Ziyan Feng / Long Yu / Yanting Tang / Weiwei Wang / Lu Yu / Changlin Tian / Ting Ran / Hongming Chen / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong /
Abstract: Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been ...Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been shown to cause mitochondrial disease and some types of cancers. However, the structure of this complex is yet to be resolved, hindering a comprehensive understanding of the functional aspects of this molecular machine. Here, we have determined the structure of human complex II in the presence of ubiquinone at 2.86 Å resolution by cryoelectron microscopy, showing it comprises two water-soluble subunits, SDHA and SDHB, and two membrane-spanning subunits, SDHC and SDHD. This structure allows us to propose a route for electron transfer. In addition, clinically relevant mutations are mapped onto the structure. This mapping provides a molecular understanding to explain why these variants have the potential to produce disease.
History
DepositionSep 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 10, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,35311
Polymers140,1574
Non-polymers3,1967
Water00
1


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

-
Components

-
Succinate dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ABD

#1: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Flavoprotein subunit of complex II / Fp


Mass: 72786.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHA, SDH2, SDHF / Production host: Homo sapiens (human) / References: UniProt: P31040, succinate dehydrogenase
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial


Mass: 31674.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHB / Production host: Homo sapiens (human) / References: UniProt: P21912
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial


Mass: 17063.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHD / Production host: Homo sapiens (human) / References: UniProt: O14521

-
Protein , 1 types, 1 molecules C

#3: Protein Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Integral membrane protein CII-3 / QPs-1 / QPs1 / Succinate dehydrogenase complex subunit C / ...Integral membrane protein CII-3 / QPs-1 / QPs1 / Succinate dehydrogenase complex subunit C / Succinate-ubiquinone oxidoreductase cytochrome B large subunit / CYBL


Mass: 18632.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHC, CYB560, SDH3 / Production host: Homo sapiens (human) / References: UniProt: Q99643

-
Non-polymers , 7 types, 7 molecules

#5: Chemical ChemComp-FAD / 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
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O4
#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H78NO8P / Comment: POPE, phospholipid*YM

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: The human mitochondrial complex II, composed of SDHA, SDHB, SDHC and SDHD
Type: COMPLEX / Entity ID: #1, #4, #3, #2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114967 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0118843
ELECTRON MICROSCOPYf_angle_d1.12811994
ELECTRON MICROSCOPYf_dihedral_angle_d23.3573233
ELECTRON MICROSCOPYf_chiral_restr0.0631295
ELECTRON MICROSCOPYf_plane_restr0.0141516

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more