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- PDB-8rr0: CryoEM structure of Molybdenum bispyranopterin guanine dinucleoti... -

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Basic information

Entry
Database: PDB / ID: 8rr0
TitleCryoEM structure of Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1 from Bacillus subtilis
Components
  • Probable oxidoreductase YjgC
  • Uncharacterized protein YjgD
KeywordsOXIDOREDUCTASE / Bacterial metabolism Bioenergetics Metalloenzyme Quinone Iron-Sulfur Cluster Helical Membrane Plug-in
Function / homology
Function and homology information


formate metabolic process / formate dehydrogenase (NAD+) activity / Oxidoreductases / molybdopterin cofactor binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / membrane
Similarity search - Function
Protein of unknown function DUF1641 / Protein of unknown function (DUF1641) / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region ...Protein of unknown function DUF1641 / Protein of unknown function (DUF1641) / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / Aspartate decarboxylase-like domain superfamily / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
UNDECANOIC ACID / MOLYBDENUM(IV) ION / : / FE2/S2 (INORGANIC) CLUSTER / HYDROSULFURIC ACID / nonanoic acid / Chem-MGD / MENAQUINONE-7 / MYRISTIC ACID / IRON/SULFUR CLUSTER ...UNDECANOIC ACID / MOLYBDENUM(IV) ION / : / FE2/S2 (INORGANIC) CLUSTER / HYDROSULFURIC ACID / nonanoic acid / Chem-MGD / MENAQUINONE-7 / MYRISTIC ACID / IRON/SULFUR CLUSTER / HEPTANOIC ACID / Uncharacterized protein YjgD / Probable oxidoreductase YjgC
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsCherrier, M.V. / Arnoux, P. / Martin, L. / Nicolet, Y. / Schoehn, G. / Legrand, P. / Broc, M. / Seduk, F. / Brasseur, G. / Arias-Cartin, R. ...Cherrier, M.V. / Arnoux, P. / Martin, L. / Nicolet, Y. / Schoehn, G. / Legrand, P. / Broc, M. / Seduk, F. / Brasseur, G. / Arias-Cartin, R. / Magalon, A. / Walburger, A. / Uzel, A. / Guigliarelli, B. / Grimaldi, S. / Pierrel, F. / Mate, M.
Funding support France, 7items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-10-LABX-49-01 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0035-01 France
Centre National de la Recherche Scientifique (CNRS)MICROBIOCO2 France
Agence Nationale de la Recherche (ANR)ANR 16-CE29-0010-01 France
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: A scaffold for quinone channeling between membrane and soluble bacterial oxidoreductases.
Authors: M Broc / M V Cherrier / A Uzel / R Arias-Cartin / P Arnoux / G Brasseur / F Seduk / B Guigliarelli / P Legrand / F Pierrel / G Schoehn / M J Maté / L Martin / S Grimaldi / Y Nicolet / A Magalon / A Walburger /
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 ...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.
History
DepositionJan 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.2Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YjgD
B: Probable oxidoreductase YjgC
C: Uncharacterized protein YjgD
D: Probable oxidoreductase YjgC
E: Uncharacterized protein YjgD
F: Probable oxidoreductase YjgC
G: Uncharacterized protein YjgD
H: Probable oxidoreductase YjgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,374100
Polymers524,9338
Non-polymers31,44192
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Uncharacterized protein YjgD


Mass: 21308.650 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34681
#2: Protein
Probable oxidoreductase YjgC


Mass: 109924.477 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34720, Oxidoreductases

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Non-polymers , 12 types, 176 molecules

#3: Chemical...
ChemComp-11A / UNDECANOIC ACID


Mass: 186.291 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: C11H22O2
#4: Chemical
ChemComp-A1H2V / [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate / (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL / NEOMYCIN A / NEAMINE / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside


Mass: 751.023 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H79O10P
#5: Chemical
ChemComp-SHV / HEPTANOIC ACID


Mass: 130.185 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H14O2
#6: Chemical
ChemComp-KNA / nonanoic acid


Mass: 158.238 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H18O2
#7: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#8: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-4MO / MOLYBDENUM(IV) ION


Mass: 95.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C46H64O2 / Feature type: SUBJECT OF INVESTIGATION
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.524244 MDa / Experimental value: NO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Buffer solutionpH: 6 / Details: 50 mM MES pH 6 50mM Na2SO4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMMES1
250 mMSodium sulfateNa2SO41
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA / Grid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4977
Image scansMovie frames/image: 40 / Used frames/image: 2-40

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.2.particle selection
4cryoSPARC3.3.2.CTF correction
7PHENIX1.20.1.model fitting
10cryoSPARC3.3.2.final Euler assignment
11cryoSPARC3.3.2.classification
12cryoSPARC3.3.2.3D reconstruction
19PHENIX1.20.1.model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112095 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingPDB-ID: 8RQZ

8rqz


Accession code: 8RQZ / Source name: PDB / Type: experimental model

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