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- EMDB-19452: CryoEM structure of Molybdenum bispyranopterin guanine dinucleoti... -

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Basic information

Entry
Database: EMDB / ID: EMD-19452
TitleCryoEM structure of Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1 from Bacillus subtilis
Map data
Sample
  • Complex: Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1
    • Protein or peptide: x 2 types
  • Ligand: x 12 types
KeywordsBacterial metabolism Bioenergetics Metalloenzyme Quinone Iron-Sulfur Cluster Helical Membrane Plug-in / OXIDOREDUCTASE
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
Uncharacterized protein YjgD / Probable oxidoreductase YjgC
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsCherrier MV / Arnoux P / Martin L / Nicolet Y / Schoehn G / Legrand P / Broc M / Seduk F / Brasseur G / Arias-Cartin R ...Cherrier MV / 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, 7 items
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 MV / 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, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19452.png

Downloads & links

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Map

FileDownload / File: emd_19452.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.6688908 - 2.4085891
Average (Standard dev.)0.0020752063 (±0.03724655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19452_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19452_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Molybdenum bispyranopterin guanine dinucleotide formate dehydroge...

EntireName: Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1
Components
  • Complex: Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1
    • Protein or peptide: Uncharacterized protein YjgD
    • Protein or peptide: Probable oxidoreductase YjgC
  • Ligand: UNDECANOIC ACID
  • Ligand: [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate
  • Ligand: HEPTANOIC ACID
  • Ligand: nonanoic acid
  • Ligand: MYRISTIC ACID
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
  • Ligand: MOLYBDENUM(IV) ION
  • Ligand: HYDROSULFURIC ACID
  • Ligand: MENAQUINONE-7
  • Ligand: water

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Supramolecule #1: Molybdenum bispyranopterin guanine dinucleotide formate dehydroge...

SupramoleculeName: Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 524.244 KDa

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Macromolecule #1: Uncharacterized protein YjgD

MacromoleculeName: Uncharacterized protein YjgD / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 21.30865 KDa
SequenceString:
MAKAIKRIQK IEVTEEDQRK RDLREIEDAL IDHKEAILET LHMLGHMNER GVLPLLRGLF GQGDKVLDIL VKKADTEETA NTLKNLLLL FGTLGMLDVK QLEPLILKVN AGVASAVEQK NSEEKTGYFD IIRSLKDPEI NKSITLLFSF LKGMGQDTKE L ERTTQPPE HQKHHQEPRE KRGMNKRD

UniProtKB: Uncharacterized protein YjgD

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Macromolecule #2: Probable oxidoreductase YjgC

MacromoleculeName: Probable oxidoreductase YjgC / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: Oxidoreductases
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 109.924477 KDa
SequenceString: MAGKKTITIN GVEMEASEEQ TVLQLLNNSS IEVPQVCYHP SLGPIETCDT CIVSINGELK RSCSAELKDG DVIDTLSPDV KKAQVIGMD KILYNHELYC TVCDYNNGGC EIHNTVKEMK INHQSIPFDH KPYHKDESHP FYRYDPDQCI LCGRCVEACQ D VQVTETLT ...String:
MAGKKTITIN GVEMEASEEQ TVLQLLNNSS IEVPQVCYHP SLGPIETCDT CIVSINGELK RSCSAELKDG DVIDTLSPDV KKAQVIGMD KILYNHELYC TVCDYNNGGC EIHNTVKEMK INHQSIPFDH KPYHKDESHP FYRYDPDQCI LCGRCVEACQ D VQVTETLT IDWERKRPRV IWDNDVPINE SSCVSCGHCS TVCPCNAMME KGMEGEAGYL TGINNETLRP MIEITKGVET GY GSILAIS DMESAMRDER IKKTKTVCTY CGVGCSFDVW TKGRDILKVE PQEEAPANGI STCVKGKFGW DFVNSEERLT KPL IREGDH FREAEWEEAL LLIASKFTEL KEAFGPDSLA FITSSKCTNE ESYLMQKLAR GVIGTNNVDN CSRYCQSPAT AGLF RTVGY GGDSGSITDI AQADLVLIIG SNTSESHPVL STRIKRAHKL RGQKVIVADI RKHEMAERSD LFVQPRAGSD IVWLN AIAK YLIENGKADE RFLRERVNGR DEYVKSLAPY TLEYAEEKTG IDQETLIQMA EMIGQADSVC ALWAMGVTQH IGGSDT STA ISNLLLVTGN YGKPGAGSYP LRGHNNVQGA SDFGSMPDRL PGYEKVTDEQ VRQKYERVWG VPLPKEPGMT NHEMIEK IH SGQLKAMYVK GEEMGLVDSN INHVHAAYEK LDFFVVQDIF LSRTAEFADV VLPASPSLEK EGTFTNTERR IQRLYQVF E PLGESKPDWQ IIMEVANKLG AGWLYEHPAD IMEEAAKLSP IYAGVTYERL EGYNSLQWPV NADGKDSPLL FTERFPFPD GKAILYPVQW TEPKEFGEEY DIHVNNGRLL EHFHEGNLTY KSKGISEKTP EVFLEISPEL AAERGIQDGT LVRLTSPFGN VKVKCLITD RVKGKEVYLP MNDSGEAAIN LLTGSHADKD TDTPAYKETS AKMEILKHDG ISPLPKINHR NGNPQPQIGV Q VHKKWARK DYIFPGDAVK RGMGHNG

UniProtKB: Probable oxidoreductase YjgC

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Macromolecule #3: UNDECANOIC ACID

MacromoleculeName: UNDECANOIC ACID / type: ligand / ID: 3 / Number of copies: 24 / Formula: 11A
Molecular weightTheoretical: 186.291 Da
Chemical component information

ChemComp-11A:
UNDECANOIC ACID / antifungal*YM

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Macromolecule #4: [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphory...

MacromoleculeName: [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate
type: ligand / ID: 4 / Number of copies: 12 / Formula: A1H2V
Molecular weightTheoretical: 751.023 Da

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Macromolecule #5: HEPTANOIC ACID

MacromoleculeName: HEPTANOIC ACID / type: ligand / ID: 5 / Number of copies: 8 / Formula: SHV
Molecular weightTheoretical: 130.185 Da
Chemical component information

ChemComp-SHV:
HEPTANOIC ACID

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Macromolecule #6: nonanoic acid

MacromoleculeName: nonanoic acid / type: ligand / ID: 6 / Number of copies: 4 / Formula: KNA
Molecular weightTheoretical: 158.238 Da
Chemical component information

ChemComp-KNA:
nonanoic acid

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Macromolecule #7: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 7 / Number of copies: 4 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

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Macromolecule #8: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 8 / Number of copies: 4 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / Number of copies: 16 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #10: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,1...

MacromoleculeName: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
type: ligand / ID: 10 / Number of copies: 8 / Formula: MGD
Molecular weightTheoretical: 740.557 Da
Chemical component information

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

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Macromolecule #11: MOLYBDENUM(IV) ION

MacromoleculeName: MOLYBDENUM(IV) ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: 4MO
Molecular weightTheoretical: 95.94 Da
Chemical component information

ChemComp-4MO:
MOLYBDENUM(IV) ION

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Macromolecule #12: HYDROSULFURIC ACID

MacromoleculeName: HYDROSULFURIC ACID / type: ligand / ID: 12 / Number of copies: 4 / Formula: H2S
Molecular weightTheoretical: 34.081 Da
Chemical component information

ChemComp-H2S:
HYDROSULFURIC ACID

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Macromolecule #13: MENAQUINONE-7

MacromoleculeName: MENAQUINONE-7 / type: ligand / ID: 13 / Number of copies: 4 / Formula: MQ7
Molecular weightTheoretical: 648.999 Da
Chemical component information

ChemComp-MQ7:
MENAQUINONE-7

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Macromolecule #14: water

MacromoleculeName: water / type: ligand / ID: 14 / Number of copies: 84 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 6
Component:
ConcentrationNameFormula
50.0 mMMES
50.0 mMSodium sulfateNa2SO4

Details: 50 mM MES pH 6 50mM Na2SO4
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 30 mA
VitrificationCryogen name: PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 2-40 / Number grids imaged: 1 / Number real images: 4977 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2.) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2.) / Number images used: 112095
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2.)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.3.2.)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8rqz


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-8rr0:
CryoEM structure of Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1 from Bacillus subtilis

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