9LAY | pdb_00009lay

Cryo-EM structure of the apo-form succinate dehydrogenase from Chloroflexus aurantiacus

PDB DOI: https://doi.org/10.2210/pdb9LAY/pdb
EM Map EMD-62932: 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: 2.62 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: 400.7 kDa
Atom Count: 27,237
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 9 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 U [auth D] SDF format, chain J [auth A] SDF format, chain EA [auth G] MOL2 format, chain U [auth D] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth G] mmCIF format, chain U [auth D] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth G]	EA [auth G], J [auth A], U [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain EA [auth G] Focus chain J [auth A] Focus chain U [auth D] Interactions & Density Focus chain EA [auth G] Focus chain J [auth A] Focus chain U [auth D]
PGV (Subject of Investigation/LOI) Query on PGV Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain R [auth C] SDF format, chain MA [auth I] MOL2 format, chain Y [auth E] MOL2 format, chain R [auth C] MOL2 format, chain MA [auth I] mmCIF format, chain Y [auth E] mmCIF format, chain R [auth C] mmCIF format, chain MA [auth I]	MA [auth I], R [auth C], Y [auth E]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain MA [auth I] Focus chain R [auth C] Focus chain Y [auth E] Interactions & Density Focus chain MA [auth I] Focus chain R [auth C] Focus chain Y [auth E]
PEV (Subject of Investigation/LOI) Query on PEV Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain S [auth C] SDF format, chain IA [auth I] MOL2 format, chain Z [auth F] MOL2 format, chain S [auth C] MOL2 format, chain IA [auth I] mmCIF format, chain Z [auth F] mmCIF format, chain S [auth C] mmCIF format, chain IA [auth I]	IA [auth I], S [auth C], Z [auth F]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₃₉ H₇₈ N O₈ P RPJZYOHZALDGKI-QNGWXLTQSA-N		Interactions Focus chain IA [auth I] Focus chain S [auth C] Focus chain Z [auth F] Interactions & Density Focus chain IA [auth I] Focus chain S [auth C] Focus chain Z [auth F]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain KA [auth I] SDF format, chain JA [auth I] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain KA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain KA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] JA [auth I] KA [auth I] O [auth C] AA [auth F], BA [auth F], JA [auth I], KA [auth I], O [auth C], P [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain O [auth C] Focus chain P [auth C]
LMT (Subject of Investigation/LOI) Query on LMT Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain LA [auth I] SDF format, chain CA [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain LA [auth I] MOL2 format, chain CA [auth F] mmCIF format, chain Q [auth C] mmCIF format, chain LA [auth I] mmCIF format, chain CA [auth F]	CA [auth F], LA [auth I], Q [auth C]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain CA [auth F] Focus chain LA [auth I] Focus chain Q [auth C] Interactions & Density Focus chain CA [auth F] Focus chain LA [auth I] Focus chain Q [auth C]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain FA [auth H] SDF format, chain V [auth E] SDF format, chain L [auth B] MOL2 format, chain FA [auth H] MOL2 format, chain V [auth E] MOL2 format, chain L [auth B] mmCIF format, chain FA [auth H] mmCIF format, chain V [auth E] mmCIF format, chain L [auth B]	FA [auth H], L [auth B], V [auth E]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain FA [auth H] Focus chain L [auth B] Focus chain V [auth E] Interactions & Density Focus chain FA [auth H] Focus chain L [auth B] Focus chain V [auth E]
F3S (Subject of Investigation/LOI) Query on F3S Download Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain N [auth B] SDF format, chain HA [auth H] MOL2 format, chain X [auth E] MOL2 format, chain N [auth B] MOL2 format, chain HA [auth H] mmCIF format, chain X [auth E] mmCIF format, chain N [auth B] mmCIF format, chain HA [auth H]	HA [auth H], N [auth B], X [auth E]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain HA [auth H] Focus chain N [auth B] Focus chain X [auth E] Interactions & Density Focus chain HA [auth H] Focus chain N [auth B] Focus chain X [auth E]
FES (Subject of Investigation/LOI) Query on FES Download Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain M [auth B] SDF format, chain GA [auth H] MOL2 format, chain W [auth E] MOL2 format, chain M [auth B] MOL2 format, chain GA [auth H] mmCIF format, chain W [auth E] mmCIF format, chain M [auth B] mmCIF format, chain GA [auth H]	GA [auth H], M [auth B], W [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain GA [auth H] Focus chain M [auth B] Focus chain W [auth E] Interactions & Density Focus chain GA [auth H] Focus chain M [auth B] Focus chain W [auth E]
SIN (Subject of Investigation/LOI) Query on SIN Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain K [auth A] SDF format, chain DA [auth G] MOL2 format, chain T [auth D] MOL2 format, chain K [auth A] MOL2 format, chain DA [auth G] mmCIF format, chain T [auth D] mmCIF format, chain K [auth A] mmCIF format, chain DA [auth G]	DA [auth G], K [auth A], T [auth D]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain DA [auth G] Focus chain K [auth A] Focus chain T [auth D] Interactions & Density Focus chain DA [auth G] Focus chain K [auth A] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.62 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