9KC4 | pdb_00009kc4

The Cryo-EM structure of human succinate dehydrogenase in complex with Benzovindiflupyr

PDB DOI: https://doi.org/10.2210/pdb9KC4/pdb
EM Map EMD-62241: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-10-31 Released: 2026-05-06
Deposition Author(s): Liu, Y., Gong, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 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

The Cryo-EM structure of human succinate dehydrogenase in complex with Benzovindiflupyr

Liu, Y., Gong, H.

To be published.

Macromolecule Content

Total Structure Weight: 143.5 kDa
Atom Count: 8,645
Modeled Residue Count: 1,090
Deposited Residue Count: 1,272
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A	664	Homo sapiens	Mutation(s): 0 Gene Names: SDHA, SDH2, SDHF EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (PDB Primary Data)
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31040
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	B	280	Homo sapiens	Mutation(s): 0 Gene Names: SDHB, SDH, SDH1 EC: 1.3.5.1 (PDB Primary Data), 1.1.5 (PDB Primary Data)
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21912
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial	C	169	Homo sapiens	Mutation(s): 0 Gene Names: SDHC, CYB560, SDH3
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99643
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	159	Homo sapiens	Mutation(s): 0 Gene Names: SDHD, SDH4
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14521
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) 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]
PEV (Subject of Investigation/LOI) Query on PEV Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₃₉ H₇₈ N O₈ P RPJZYOHZALDGKI-QNGWXLTQSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
A1EGM( Subject of Investigation/LOI) Query on A1EGM Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	(1S,4R)-benzovindiflupyr C₁₈ H₁₅ Cl₂ F₂ N₃ O CCCGEKHKTPTUHJ-VHSXEESVSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
SF4 (Subject of Investigation/LOI) 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 (Subject of Investigation/LOI) 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 (Subject of Investigation/LOI) 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]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.65 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Liu, Y.

Gong, H.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81520108019
National Natural Science Foundation of China (NSFC)	China	32100976
National Natural Science Foundation of China (NSFC)	China	82222042