9LB0 | pdb_00009lb0

Cryo-EM structure of the MK7-bound succinate dehydrogenase from Chloroflexus aurantiacus

PDB DOI: https://doi.org/10.2210/pdb9LB0/pdb
EM Map EMD-62934: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Chloroflexus aurantiacus J-10-fl
Mutation(s): No

Deposited: 2025-01-02 Released: 2025-11-12
Deposition Author(s): Zhang, X., Wu, J.Y., Xu, X.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.74 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

Structural basis of menaquinone reduction by succinate dehydrogenase from early photosynthetic bacterium Chloroflexus aurantiacus

Zhang, X., Wu, J.Y., Xu, X.L.

To be published.

Macromolecule Content

Total Structure Weight: 399.83 kDa
Atom Count: 27,158
Modeled Residue Count: 3,381
Deposited Residue Count: 3,468
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase or fumarate reductase, flavoprotein subunit	A, D, G	657	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 EC: 1.3.99.1 (PDB Primary Data), 1.3.5.1 (UniProt)
UniProt
Find proteins for A9WDT7 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WDT7 Go to UniProtKB: A9WDT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9WDT7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4Fe-4S ferredoxin iron-sulfur binding domain protein	B, E, H	260	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0
UniProt
Find proteins for A9WDT6 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WDT6 Go to UniProtKB: A9WDT6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9WDT6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family	C, F, I	239	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0
UniProt
Find proteins for A9WDT8 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WDT8 Go to UniProtKB: A9WDT8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9WDT8
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 S [auth D] SDF format, chain J [auth A] SDF format, chain BA [auth G] MOL2 format, chain S [auth D] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth G] mmCIF format, chain S [auth D] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth G]	BA [auth G], J [auth A], S [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain BA [auth G] Focus chain J [auth A] Focus chain S [auth D] Interactions & Density Focus chain BA [auth G] Focus chain J [auth A] Focus chain S [auth D]
MQ7 (Subject of Investigation/LOI) Query on MQ7 Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain JA [auth I] SDF format, chain IA [auth I] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain JA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain JA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain AA [auth F]	AA [auth F] IA [auth I] JA [auth I] Q [auth C] R [auth C] AA [auth F], IA [auth I], JA [auth I], Q [auth C], R [auth C], Z [auth F]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain AA [auth F] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain Q [auth C] Focus chain R [auth C] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain Q [auth C] Focus chain R [auth C] Focus chain Z [auth F]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain GA [auth I] SDF format, chain FA [auth I] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain GA [auth I] MOL2 format, chain FA [auth I] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain GA [auth I] mmCIF format, chain FA [auth I]	FA [auth I] GA [auth I] N [auth C] O [auth C] W [auth F] FA [auth I], GA [auth I], N [auth C], O [auth C], W [auth F], X [auth F]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain FA [auth I] Focus chain GA [auth I] Focus chain N [auth C] Focus chain O [auth C] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain FA [auth I] Focus chain GA [auth I] Focus chain N [auth C] Focus chain O [auth C] Focus chain W [auth F] Focus chain X [auth F]
LMT (Subject of Investigation/LOI) Query on LMT Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain P [auth C] SDF format, chain HA [auth I] MOL2 format, chain Y [auth F] MOL2 format, chain P [auth C] MOL2 format, chain HA [auth I] mmCIF format, chain Y [auth F] mmCIF format, chain P [auth C] mmCIF format, chain HA [auth I]	HA [auth I], P [auth C], Y [auth F]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain HA [auth I] Focus chain P [auth C] Focus chain Y [auth F] Interactions & Density Focus chain HA [auth I] Focus chain P [auth C] Focus chain Y [auth F]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain K [auth B] SDF format, chain CA [auth H] MOL2 format, chain T [auth E] MOL2 format, chain K [auth B] MOL2 format, chain CA [auth H] mmCIF format, chain T [auth E] mmCIF format, chain K [auth B] mmCIF format, chain CA [auth H]	CA [auth H], K [auth B], T [auth E]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain K [auth B] Focus chain T [auth E] Interactions & Density Focus chain CA [auth H] Focus chain K [auth B] Focus chain T [auth E]
F3S (Subject of Investigation/LOI) Query on F3S Download Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain M [auth B] SDF format, chain EA [auth H] MOL2 format, chain V [auth E] MOL2 format, chain M [auth B] MOL2 format, chain EA [auth H] mmCIF format, chain V [auth E] mmCIF format, chain M [auth B] mmCIF format, chain EA [auth H]	EA [auth H], M [auth B], V [auth E]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain EA [auth H] Focus chain M [auth B] Focus chain V [auth E] Interactions & Density Focus chain EA [auth H] Focus chain M [auth B] Focus chain V [auth E]
FES (Subject of Investigation/LOI) Query on FES Download Ideal Coordinates CCD File SDF format, chain U [auth E] SDF format, chain L [auth B] SDF format, chain DA [auth H] MOL2 format, chain U [auth E] MOL2 format, chain L [auth B] MOL2 format, chain DA [auth H] mmCIF format, chain U [auth E] mmCIF format, chain L [auth B] mmCIF format, chain DA [auth H]	DA [auth H], L [auth B], U [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain L [auth B] Focus chain U [auth E] Interactions & Density Focus chain DA [auth H] Focus chain L [auth B] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Zhang, X.

Wu, J.Y.

Xu, X.L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32471270
National Natural Science Foundation of China (NSFC)	China	32171227
National Natural Science Foundation of China (NSFC)	China	31870740