6LUM | pdb_00006lum

Structure of Mycobacterium smegmatis succinate dehydrogenase 2

• PDB DOI: https://doi.org/10.2210/pdb6LUM/pdb
• EM Map EMD-0981: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium smegmatis MC2 51
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2020-01-29 Released: 2020-05-27 
• Deposition Author(s): Gao, Y., Gong, H., Zhou, X., Xiao, Y., Wang, W., Ji, W., Wang, Q., Rao, Z.
• Funding Organization(s): Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF.

Gong, H., Gao, Y., Zhou, X., Xiao, Y., Wang, W., Tang, Y., Zhou, S., Zhang, Y., Ji, W., Yu, L., Tian, C., Lam, S.M., Shui, G., Guddat, L.W., Wong, L.L., Wang, Q., Rao, Z.

(2020) Nat Commun 11: 4245-4245

• PubMed: 32843629 
• DOI: https://doi.org/10.1038/s41467-020-18011-9
• Primary Citation Related Structures: 
  6LUM


• PubMed Abstract: 
  

  Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.

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Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353, Tianjin, China. [e-mail].
Laboratory of Structural Biology, Tsinghua University, 100084, Beijing, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353, Tianjin, China.
National Laboratory of Biomacromolecules,omolecules, Institute of Biophysics, CAS, 100101, Beijing, China.
High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China.
Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China.
State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, CAS, 100101, Beijing, China.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia.
Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. [e-mail].
National Laboratory of Biomacromolecules,omolecules, Institute of Biophysics, CAS, 100101, Beijing, China. [e-mail].
State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353, Tianjin, China. [e-mail].
Laboratory of Structural Biology, Tsinghua University, 100084, Beijing, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. [e-mail].
National Laboratory of Biomacromolecules,omolecules, Institute of Biophysics, CAS, 100101, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 15-mer - A3B3C3D3E3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 15-mer - A5B3C3D3E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 423.47 kDa 
• Atom Count: 26,191 
• Modeled Residue Count: 3,178 
• Deposited Residue Count: 3,543 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase subunit C	A [auth C], F [auth G], K [auth M]	138	Mycolicibacterium smegmatis MC2 51	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0QT10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QT10  Go to UniProtKB:  A0QT10

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase subunit D	B [auth D], G [auth H], L [auth N]	166	Mycolicibacterium smegmatis MC2 51	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0QT09 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QT09  Go to UniProtKB:  A0QT09

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase subunit F	C [auth E], H [auth I], M [auth O]	32	Mycolicibacterium smegmatis MC2 51	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0R4D1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R4D1  Go to UniProtKB:  A0R4D1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase subunit A	D [auth A], I [auth J], N [auth P]	584	Mycolicibacterium smegmatis MC2 51	Mutation(s): 0  EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for A0QT08 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QT08  Go to UniProtKB:  A0QT08

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase subunit B	E [auth B], J [auth K], O [auth Q]	261	Mycolicibacterium smegmatis MC2 51	Mutation(s): 0  EC: 1.3.5.1
UniProt
Find proteins for A0QT07 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QT07  Go to UniProtKB:  A0QT07

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL (Subject of Investigation/LOI)	HA [auth H], U [auth D], WA [auth N]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PIE (Subject of Investigation/LOI)	IA [auth H], PA [auth M], X [auth E]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol C43 H80 O13 P PDLAMJKMOKWLAJ-OJERQSHOSA-M
FAD (Subject of Investigation/LOI)	JA [auth J], XA [auth P], Y [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MQ9 (Subject of Investigation/LOI)	GA [auth H], RA [auth N], T [auth D], TA [auth N], UA [auth N], V [auth D]	MENAQUINONE-9 C56 H80 O2 WCRXHNIUHQUASO-ABFXHILCSA-N
PEV (Subject of Investigation/LOI)	BB [auth Q], CA [auth G], NA [auth K], P [auth C], Q [auth C], QA [auth M]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C39 H78 N O8 P RPJZYOHZALDGKI-QNGWXLTQSA-N
LPP	DA [auth H], VA [auth N], W [auth D]	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C35 H69 O8 P PORPENFLTBBHSG-MGBGTMOVSA-N
HEM (Subject of Investigation/LOI)	EA [auth H], FA [auth H], OA [auth M], R [auth D], S [auth D], SA [auth N]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SF4	AA [auth B], LA [auth K], ZA [auth Q]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	AB [auth Q], BA [auth B], MA [auth K]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES	KA [auth K], YA [auth Q], Z [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Gao, Y., Gong, H., Zhou, X., Xiao, Y., Wang, W., Ji, W., Wang, Q., Rao, Z.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB08020200
National Natural Science Foundation of China (NSFC)	China	81520108019, 813300237
Chinese Academy of Sciences	China	2017YFC0840300

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-10-07
  Changes: Database references, Derived calculations
• Version 2.0: 2020-12-02
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
• Version 3.0: 2021-10-20
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description
• Version 3.1: 2024-05-29
  Changes: Data collection
• Version 3.2: 2025-12-24
  Changes: Data collection, Structure summary
• Version 4.0: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary