7D6X

Mycobacterium smegmatis Sdh1 complex in the apo form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster.

Zhou, X.Gao, Y.Wang, W.Yang, X.Yang, X.Liu, F.Tang, Y.Lam, S.M.Shui, G.Yu, L.Tian, C.Guddat, L.W.Wang, Q.Rao, Z.Gong, H.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2022308118
  • Primary Citation of Related Structures:  
    7D6V, 7D6X

  • PubMed Abstract: 

    Complex II, also known as succinate dehydrogenase (SQR) or fumarate reductase (QFR), is an enzyme involved in both the Krebs cycle and oxidative phosphorylation. Mycobacterial Sdh1 has recently been identified as a new class of respiratory complex II (type F) but with an unknown electron transfer mechanism. Here, using cryoelectron microscopy, we have determined the structure of Mycobacterium smegmatis Sdh1 in the presence and absence of the substrate, ubiquinone-1, at 2.53-Å and 2.88-Å resolution, respectively. Sdh1 comprises three subunits, two that are water soluble, SdhA and SdhB, and one that is membrane spanning, SdhC. Within these subunits we identified a quinone-binding site and a rarely observed Rieske-type [2Fe-2S] cluster, the latter being embedded in the transmembrane region. A mutant, where two His ligands of the Rieske-type [2Fe-2S] were changed to alanine, abolished the quinone reduction activity of the Sdh1. Our structures allow the proposal of an electron transfer pathway that connects the substrate-binding and quinone-binding sites. Given the unique features of Sdh1 and its essential role in Mycobacteria , these structures will facilitate antituberculosis drug discovery efforts that specifically target this complex.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase subunit A635Mycolicibacterium smegmatisMutation(s): 0 
EC: 1.3
UniProt
Find proteins for A0QPJ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QPJ3 
Go to UniProtKB:  A0QPJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QPJ3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fumarate reductase iron-sulfur subunit249Mycolicibacterium smegmatisMutation(s): 0 
UniProt
Find proteins for A0QPJ2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QPJ2 
Go to UniProtKB:  A0QPJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QPJ2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase (Membrane anchor subunit)283Mycolicibacterium smegmatisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0QPJ4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QPJ4 
Go to UniProtKB:  A0QPJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QPJ4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

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

Download Ideal Coordinates CCD File 
H [auth C](1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
SF4
Query on SF4

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

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 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 SciencesChinaXDB37030201, XDB37020203
National Natural Science Foundation of China (NSFC)China81520108019, 813300237
Chinese Academy of SciencesChina2017YFC0840300

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references