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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 / Aspartate decarboxylase-like domain superfamily / 2Fe-2S iron-sulfur cluster binding domain / 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: To Be Published
Title: Conserved Helical Membrane Plug-in for Quinone reductases
Authors: Cherrier, M.V. / Arnoux, P. / Martin, L. / Nicolet, Y. / Schoehn, G. / Broc, M. / Seduk, F. / Brasseur, G. / Arias-Cartin, R. / Magalon, A. / Walburger, A. / Uzel, A. / Guigliarelli, B. / ...Authors: Cherrier, M.V. / Arnoux, P. / Martin, L. / Nicolet, Y. / Schoehn, G. / Broc, M. / Seduk, F. / Brasseur, G. / Arias-Cartin, R. / Magalon, A. / Walburger, A. / Uzel, A. / Guigliarelli, B. / Grimaldi, S. / Pierrel, F. / Mate, M.
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

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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 / Comment: antifungal*YM
#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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