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- EMDB-64903: Cryo-EM structure of formate dehydrogenase from Shewanella oneide... -

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Basic information

Entry
Database: EMDB / ID: EMD-64903
TitleCryo-EM structure of formate dehydrogenase from Shewanella oneidensis MR-1 (SoFdhAB)
Map data
Sample
  • Complex: Heterodimer composed of formate dehydrogenase molybdopterin-binding subunit FdhA and 4Fe-4S dicluster domain-containing protein
    • Protein or peptide: Formate dehydrogenase molybdopterin-binding subunit FdhA
    • Protein or peptide: 4Fe-4S dicluster domain-containing protein
  • 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: IRON/SULFUR CLUSTER
  • Ligand: HYDROSULFURIC ACID
  • Ligand: TUNGSTEN ION
KeywordsFormate dehydrogenase / carbon dioxide reduction / tungsten (W)-dependent / OXIDOREDUCTASE
Function / homology
Function and homology information


formate dehydrogenase-N / formate dehydrogenase (quinone) activity / formate oxidation / formate dehydrogenase complex / molybdopterin cofactor binding / cell envelope / anaerobic respiration / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase ...Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Formate dehydrogenase molybdopterin-binding subunit FdhA
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsLiu W / Zhang L
Funding support China, 2 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDC0120103 China
Chinese Academy of SciencesYSBR 072-3 China
CitationJournal: Nat Commun / Year: 2026
Title: An interfacial-intramolecular electron highway for accelerated electrocatalytic CO reduction by an O-tolerant formate dehydrogenase.
Authors: Weisong Liu / Peng Zhang / Xiufeng Wang / Kuncheng Zhang / Wenhua Yang / Huijuan Cui / Jun Liu / Junsong Sun / Chun You / Haiyang Cui / Zhiguang Zhu / Lingling Zhang /
Abstract: Bioelectrocatalytic CO reduction offers a sustainable route for CO bioconversion, yet remains limited by interfacial-intramolecular electron transfer and oxygen sensitivity. Here, we mine a formate ...Bioelectrocatalytic CO reduction offers a sustainable route for CO bioconversion, yet remains limited by interfacial-intramolecular electron transfer and oxygen sensitivity. Here, we mine a formate dehydrogenase from Shewanella oneidensis MR-1 (SoFdhAB) featuring completely oxygen tolerant and direct-electron-transfer (DET) electrocatalytic performances. Cryo-electron microscopy (Cryo-EM) analysis reveals an intramolecular electron highway comprising five [4Fe-4S] clusters, a regional face-face contact facilitating interfacial ET, and a unique oxygen resistance mechanism different from inactivation-activation. By acquiring a beneficial variant SoFdhAB-Y94S, a direct bioelectrocatalytic CO reduction system is constructed, accumulating 2.88 ± 0.03 mmol formate in 64 hours with a steady rate of 45.3 ± 0.5 μmol h cm and a Faradaic efficiency of 93.1 ± 5.2%. The merits of oxygen tolerance and efficient (electro)catalytic property endow SoFdhAB a robust enzyme adopted in potential application scenarios, and the inherent DET capability may inspire the interfacial engineering of other oxidoreductases.
History
DepositionJun 3, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64903.png

Downloads & links

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Map

FileDownload / File: emd_64903.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0922
Minimum - Maximum-0.5129547 - 2.1843598
Average (Standard dev.)0.000893357 (±0.037785403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64903_additional_1.map
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Half map: #2

Fileemd_64903_half_map_1.map
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Half map: #1

Fileemd_64903_half_map_2.map
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Sample components

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Entire : Heterodimer composed of formate dehydrogenase molybdopterin-bindi...

EntireName: Heterodimer composed of formate dehydrogenase molybdopterin-binding subunit FdhA and 4Fe-4S dicluster domain-containing protein
Components
  • Complex: Heterodimer composed of formate dehydrogenase molybdopterin-binding subunit FdhA and 4Fe-4S dicluster domain-containing protein
    • Protein or peptide: Formate dehydrogenase molybdopterin-binding subunit FdhA
    • Protein or peptide: 4Fe-4S dicluster domain-containing protein
  • 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: IRON/SULFUR CLUSTER
  • Ligand: HYDROSULFURIC ACID
  • Ligand: TUNGSTEN ION

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Supramolecule #1: Heterodimer composed of formate dehydrogenase molybdopterin-bindi...

SupramoleculeName: Heterodimer composed of formate dehydrogenase molybdopterin-binding subunit FdhA and 4Fe-4S dicluster domain-containing protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 122 KDa

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Macromolecule #1: Formate dehydrogenase molybdopterin-binding subunit FdhA

MacromoleculeName: Formate dehydrogenase molybdopterin-binding subunit FdhA
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase-N
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 105.996156 KDa
Recombinant expressionOrganism: Shewanella oneidensis MR-1 (bacteria)
SequenceString: MRLTRKTDPV VEPKVPALGL NRRQFLKSAG LATGGIAAAS MLGTGMMRKA EAKDIPHNAP TEVKRTICSH CSVGCGVYAE VQNGVWTGQ EPAFDHPFNQ GGHCAKGAAL REHGHGEKRL KYPMKLEGGK WKKISWDQAI NEVGDKMMAI RQESGPDSIY F MGSAKFSN ...String:
MRLTRKTDPV VEPKVPALGL NRRQFLKSAG LATGGIAAAS MLGTGMMRKA EAKDIPHNAP TEVKRTICSH CSVGCGVYAE VQNGVWTGQ EPAFDHPFNQ GGHCAKGAAL REHGHGEKRL KYPMKLEGGK WKKISWDQAI NEVGDKMMAI RQESGPDSIY F MGSAKFSN EQAYLYRKFA ALWGTNNVDH SARICHSTTV AGVANTWGYG AQTNSVNDIR HSKCILFVGS NPSEAHPVAM QH ILVAKER GAKIIVVDPR FTRTAAKSDE YVHIRPGTDI PFIYGLLWHI FENGWEDKDF IKRRVYGMER IREEVKKYTP EEV ENVVGA PKAQMYRVAK MMAETKPGSI VWCMGGTQHH VGNANTRSYC ILQLALGNMG VTGGGTNIFR GHDNVQGASD FGLS FDDLP GYFGLTSGSW AHWANVWDLD PKWVTSRFDQ GEYLGQSPQT SPGIPCSRWH DGVLEDKTKI AQKDNIRLAF FWGQS VNTE TRGREVRQAL DKMDTVVVVD PFPTMAGVMH QRKDGVYLLP AATQFETYGS VSATNRSIQW RSKVIEPLFE SLPDHV IMC KLAKKVGIDK ELFKHIKVNG EEPLIEDIVR EYNRGMWTIG YTGQSPERLK MHQENWGTFN VDSLEAPGGP AKGETYG LP WPCWGTPEMK HPGSHILYNE TKHVKDGGGS FRARFGVERN GVNLLSEEAY SAGSEIQDGY PEFTADMLKQ LGWWDDLT E DEKKYAEGKN WKTDISGGIQ RVVIKHGCIP YGNGKARAVV WNFPDDIPLH REPLYTPRRD LVAKYPTYED RMVARLPTL YKSIQDKDFA KDFPLALTSG RLVEYEGGGE ETRSNPWLAE LQQEMFIEIS PADAADRGIR DGDNVFVHSP EGAKITVKAM VTPRVVPGE CFMPYHFAGV FEGESLAKNY PEGTVPYVIG ESANTILTYG YDVVTQMQET KSSLCQISKA

UniProtKB: Formate dehydrogenase molybdopterin-binding subunit FdhA

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Macromolecule #2: 4Fe-4S dicluster domain-containing protein

MacromoleculeName: 4Fe-4S dicluster domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 22.411707 KDa
Recombinant expressionOrganism: Shewanella oneidensis MR-1 (bacteria)
SequenceString: MAVMKFLCDT KRCIECNGCV TACKNENDSA LEWGIQRRRV VTINDGQPGE ASISVACMHC TDAPCMAVCP ADCFYRTDDG IVLHNKDTC IGCGYCFYAC PFGAPQFPKK TAFGSRGKMD KCTFCAGGPE ETFSEAEHKK YGANRIAEGK LPMCAELCAT K ALLAGDAE ...String:
MAVMKFLCDT KRCIECNGCV TACKNENDSA LEWGIQRRRV VTINDGQPGE ASISVACMHC TDAPCMAVCP ADCFYRTDDG IVLHNKDTC IGCGYCFYAC PFGAPQFPKK TAFGSRGKMD KCTFCAGGPE ETFSEAEHKK YGANRIAEGK LPMCAELCAT K ALLAGDAE VVSNIYRQRM ASRGNPNVIW GYNPKTGEIN HHHHHH

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Macromolecule #3: 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: 3 / Number of copies: 2 / 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 #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 5 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #5: HYDROSULFURIC ACID

MacromoleculeName: HYDROSULFURIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: H2S
Molecular weightTheoretical: 34.081 Da
Chemical component information

ChemComp-H2S:
HYDROSULFURIC ACID

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Macromolecule #6: TUNGSTEN ION

MacromoleculeName: TUNGSTEN ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: W
Molecular weightTheoretical: 183.84 Da

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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

Concentration0.5 mg/mL
BufferpH: 8 / Details: 0.1 M Tris-HCl, 0.1 M NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138699
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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