8RR0 | pdb_00008rr0

CryoEM structure of Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1 from Bacillus subtilis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A scaffold for quinone channeling between membrane and soluble bacterial oxidoreductases.

Broc, M.Cherrier, M.V.Uzel, A.Arias-Cartin, R.Arnoux, P.Brasseur, G.Seduk, F.Guigliarelli, B.Legrand, P.Pierrel, F.Schoehn, G.Mate, M.J.Martin, L.Grimaldi, S.Nicolet, Y.Magalon, A.Walburger, A.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01607-4
  • Primary Citation of Related Structures:  
    8RQZ, 8RR0, 9GZQ

  • PubMed Abstract: 

    Redox processes are at the heart of energetic metabolism that drives life on earth. By extension, complex and efficient electron transfer wires are necessary to connect the various metabolic pathways that are often located in distinct cellular compartments. Here, we uncovered a structural module that enables channeling of quinones from the membrane to various water-soluble redox catalytic units in prokaryotes. Using X-ray crystallography and cryo-electron microscopy, we determined the structure of the unusual bacterial formate dehydrogenase ForCE that contains four ForC catalytic subunits docked around a membrane-associated tetrameric ForE central scaffold. In the latter, a conserved domain that we propose to name helical membrane plugin (HMP) was identified as essential to link formate oxidation, in Bacillus subtilis, to the aerobic respiratory chain. Our bioinformatic analysis indicates that this HMP is associated with different quinone-reducing oxidoreductases, highlighting its broad importance as a functional unit to wire electrons between a given catalytic redox center and the quinone pool.


  • Organizational Affiliation
    • Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YjgD
A, C, E, G
186Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for O34681 (Bacillus subtilis (strain 168))
Explore O34681 
Go to UniProtKB:  O34681
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34681
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable oxidoreductase YjgC
B, D, F, H
985Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
EC: 1
UniProt
Find proteins for O34720 (Bacillus subtilis (strain 168))
Explore O34720 
Go to UniProtKB:  O34720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34720
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H2V
Query on A1H2V

Download Ideal Coordinates CCD File 
AC [auth G]
CC [auth G]
DB [auth E]
DC [auth G]
FB [auth E]
AC [auth G],
CC [auth G],
DB [auth E],
DC [auth G],
FB [auth E],
GA [auth C],
GB [auth E],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
U [auth A]
[(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate
C40 H79 O10 P
WYVBOKLMHDFYQD-XPSQVAKYSA-N
MGD (Subject of Investigation/LOI)
Query on MGD

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AA [auth B]
BA [auth B]
RC [auth H]
SC [auth H]
UB [auth F]
AA [auth B],
BA [auth B],
RC [auth H],
SC [auth H],
UB [auth F],
VB [auth F],
XA [auth D],
YA [auth D]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
MQ7 (Subject of Investigation/LOI)
Query on MQ7

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BB [auth D],
EA [auth B],
VC [auth H],
YB [auth F]
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
NC [auth H]
OC [auth H]
PC [auth H]
QB [auth F]
QC [auth H]
NC [auth H],
OC [auth H],
PC [auth H],
QB [auth F],
QC [auth H],
RB [auth F],
SB [auth F],
TA [auth D],
TB [auth F],
UA [auth D],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
Y [auth B],
Z [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MYR
Query on MYR

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CB [auth E],
FA [auth C],
T [auth A],
ZB [auth G]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
11A
Query on 11A

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BC [auth G]
EB [auth E]
GC [auth G]
HA [auth C]
HC [auth G]
BC [auth G],
EB [auth E],
GC [auth G],
HA [auth C],
HC [auth G],
I [auth A],
JB [auth E],
JC [auth G],
KB [auth E],
KC [auth G],
LC [auth G],
MA [auth C],
MB [auth E],
N [auth A],
NA [auth C],
NB [auth E],
O [auth A],
OB [auth E],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
S [auth A]
UNDECANOIC ACID
C11 H22 O2
ZDPHROOEEOARMN-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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MC [auth H],
PB [auth F],
SA [auth D],
V [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
KNA
Query on KNA

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IC [auth G],
LB [auth E],
OA [auth C],
P [auth A]
nonanoic acid
C9 H18 O2
FBUKVWPVBMHYJY-UHFFFAOYSA-N
SHV
Query on SHV

Download Ideal Coordinates CCD File 
EC [auth G]
FC [auth G]
HB [auth E]
IB [auth E]
KA [auth C]
EC [auth G],
FC [auth G],
HB [auth E],
IB [auth E],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A]
HEPTANOIC ACID
C7 H14 O2
MNWFXJYAOYHMED-UHFFFAOYSA-N
4MO (Subject of Investigation/LOI)
Query on 4MO

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CA [auth B],
TC [auth H],
WB [auth F],
ZA [auth D]
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)
Query on H2S

Download Ideal Coordinates CCD File 
AB [auth D],
DA [auth B],
UC [auth H],
XB [auth F]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.2.
MODEL REFINEMENTPHENIX1.20.1.

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-15-IDEX-02
Agence Nationale de la Recherche (ANR)FranceANR-15-IDEX-02
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-10-LABX-49-01
Agence Nationale de la Recherche (ANR)FranceANR-22-CE44-0035-01
Centre National de la Recherche Scientifique (CNRS)FranceMICROBIOCO2
Agence Nationale de la Recherche (ANR)FranceANR 16-CE29-0010-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-03
    Changes: Data collection, Database references