9XEB | pdb_00009xeb

Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in YF241131B-bound state

PDB DOI: https://doi.org/10.2210/pdb9XEB/pdb
EM Map EMD-66786: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2025-10-27 Released: 2026-11-04
Deposition Author(s): Li, Z.W., Ye, Y., Yang, G.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

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 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in YF241131B-bound state

Li, Z.W., Ye, Y., Yang, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 126.39 kDa
Atom Count: 8,828
Modeled Residue Count: 1,107
Deposited Residue Count: 1,107
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A	595	Saccharomyces cerevisiae	Mutation(s): 0 EC: 1.3.5.1
UniProt
Find proteins for Q00711 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00711 Go to UniProtKB: Q00711
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00711
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	B	237	Saccharomyces cerevisiae	Mutation(s): 0 EC: 1.3.5.1
UniProt
Find proteins for P21801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21801 Go to UniProtKB: P21801
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21801
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sdh3p	C	144	Saccharomyces cerevisiae	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial	D	131	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P37298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P37298 Go to UniProtKB: P37298
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37298
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEE Query on PEE Download:Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
A1E0G (Subject of Investigation/LOI) Query on A1E0G Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	3-[bis(fluoranyl)methyl]-~{N}-[(1~{S},2~{R})-2-[2-chloranyl-4-(trifluoromethyl)phenoxy]cyclopentyl]-~{N}-cyclopropyl-5-fluoranyl-1-methyl-pyrazole-4-carboxamide C₂₁ H₂₀ Cl F₆ N₃ O₂ CQRIJLJWLSULBT-DZGCQCFKSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]