8GS8

cryo-EM structure of the human respiratory complex II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of the human respiratory complex II.

Du, Z.Zhou, X.Lai, Y.Xu, J.Zhang, Y.Zhou, S.Feng, Z.Yu, L.Tang, Y.Wang, W.Yu, L.Tian, C.Ran, T.Chen, H.Guddat, L.W.Liu, F.Gao, Y.Rao, Z.Gong, H.

(2023) Proc Natl Acad Sci U S A 120: e2216713120-e2216713120

  • DOI: https://doi.org/10.1073/pnas.2216713120
  • Primary Citation of Related Structures:  
    8GS8

  • PubMed 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 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.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300353, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial664Homo sapiensMutation(s): 0 
Gene Names: SDHASDH2SDHF
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P31040 (Homo sapiens)
Explore P31040 
Go to UniProtKB:  P31040
PHAROS:  P31040
GTEx:  ENSG00000073578 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31040
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial280Homo sapiensMutation(s): 0 
Gene Names: SDHB
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21912 (Homo sapiens)
Explore P21912 
Go to UniProtKB:  P21912
PHAROS:  P21912
GTEx:  ENSG00000117118 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21912
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial169Homo sapiensMutation(s): 0 
Gene Names: SDHCCYB560SDH3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99643 (Homo sapiens)
Explore Q99643 
Go to UniProtKB:  Q99643
PHAROS:  Q99643
GTEx:  ENSG00000143252 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99643
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial159Homo sapiensMutation(s): 0 
Gene Names: SDHD
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O14521 (Homo sapiens)
Explore O14521 
Go to UniProtKB:  O14521
PHAROS:  O14521
GTEx:  ENSG00000204370 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14521
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEV
Query on PEV

Download Ideal Coordinates CCD File 
K [auth D](1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
J [auth D]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4
Query on SF4

Download Ideal Coordinates CCD File 
G [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

Download Ideal Coordinates CCD File 
H [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
UQ1
Query on UQ1

Download Ideal Coordinates CCD File 
I [auth C]UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
F [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB08020200
National Natural Science Foundation of China (NSFC)China81520108019, 813300237,32100976,82222042
Chinese Academy of SciencesChina2017YFC0840300,2020YFA0707500

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release