9LAY | pdb_00009lay

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9LAY

This is version 1.1 of the entry. See complete history

Literature

Structural basis of menaquinone reduction by succinate dehydrogenase from Chloroflexus aurantiacus.

Zhang, X.Wu, J.Wang, J.He, H.Liu, A.Hong, X.Yu, Y.Pei, X.Fang, X.Xin, Y.Yu, L.Tian, C.Xu, X.

(2025) Nat Commun 16: 10782-10782

  • DOI: https://doi.org/10.1038/s41467-025-65828-3
  • Primary Citation Related Structures: 
    9LAY, 9LAZ, 9LB0, 9LB1

  • PubMed Abstract: 

    Succinate: menaquinone oxidoreductase (SQR) couples the oxidation of succinate with the reduction of menaquinone (MK) as part of the TCA cycle and the aerobic respiratory chain in MK-containing bacteria and archaea. Despite its significance, questions persist regarding the electron and proton transfer mechanisms that drive the endergonic MK reduction by succinate. In this study, we determine cryo-EM structures of succinate dehydrogenase (SDH) from Chloroflexus aurantiacus (CaSDH), a facultative filamentous anoxygenic phototroph (FAP) that forms one of the earliest branches of photosynthetic bacteria. The structures of trimeric CaSDH, resolved in both apo- and MK-bound forms, reveal a single membrane-anchoring subunit containing two b-type hemes, a canonical Q P site, and a Q D site with atypical location, configuration and specificity, each bound to MK molecules. Using structural analysis, EPR, and enzymatic assays, we uncover electron transfer pathways connecting succinate oxidation to MK reduction at the Q P and Q D sites. These findings provide structural insights into the electron and proton transfer mechanisms of MK-dependent diheme SQRs and establish a foundation for structure-based inhibitor design and antibacterial drug development targeting these enzymes.


  • Organizational Affiliation
    • Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China.

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:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase or fumarate reductase, flavoprotein subunit
A, D, G
657Chloroflexus aurantiacus J-10-flMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WDT7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
4Fe-4S ferredoxin iron-sulfur binding domain protein
B, E, H
260Chloroflexus aurantiacus J-10-flMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WDT6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase (Or fumarate reductase) cytochrome b subunit, b558 family
C, F, I
239Chloroflexus aurantiacus J-10-flMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WDT8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
EA [auth G],
J [auth A],
U [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PGV
(Subject of Investigation/LOI)

Query on PGV



Download:Ideal Coordinates CCD File
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
PEV
(Subject of Investigation/LOI)

Query on PEV



Download:Ideal Coordinates CCD File
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
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
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
LMT
(Subject of Investigation/LOI)

Query on LMT



Download:Ideal Coordinates CCD File
CA [auth F],
LA [auth I],
Q [auth C]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
FA [auth H],
L [auth B],
V [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
(Subject of Investigation/LOI)

Query on F3S



Download:Ideal Coordinates CCD File
HA [auth H],
N [auth B],
X [auth E]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES
(Subject of Investigation/LOI)

Query on FES



Download:Ideal Coordinates CCD File
GA [auth H],
M [auth B],
W [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SIN
(Subject of Investigation/LOI)

Query on SIN



Download:Ideal Coordinates CCD File
DA [auth G],
K [auth A],
T [auth D]
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32471270
National Natural Science Foundation of China (NSFC)China32171227
National Natural Science Foundation of China (NSFC)China31870740

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Data collection, Database references