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- PDB-9vap: Cryo-EM structure of formate dehydrogenase from Shewanella oneide... -

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Basic information

Entry
Database: PDB / ID: 9vap
TitleCryo-EM structure of formate dehydrogenase from Shewanella oneidensis MR-1 (SoFdhAB)
Components
  • 4Fe-4S dicluster domain-containing protein
  • Formate dehydrogenase molybdopterin-binding subunit FdhA
KeywordsOXIDOREDUCTASE / Formate dehydrogenase / carbon dioxide reduction / tungsten (W)-dependent
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
HYDROSULFURIC ACID / Chem-MGD / IRON/SULFUR CLUSTER / : / Formate dehydrogenase molybdopterin-binding subunit FdhA
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsLiu, W. / Zhang, L.
Funding support China, 2items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formate dehydrogenase molybdopterin-binding subunit FdhA
B: 4Fe-4S dicluster domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,86511
Polymers128,4082
Non-polymers3,4579
Water00
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, 2 molecules AB

#1: Protein Formate dehydrogenase molybdopterin-binding subunit FdhA


Mass: 105996.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: fdhA, SO_4509 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q8E8Z1, formate dehydrogenase-N
#2: Protein 4Fe-4S dicluster domain-containing protein


Mass: 22411.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Production host: Shewanella oneidensis MR-1 (bacteria)

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Non-polymers , 4 types, 9 molecules

#3: 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.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION

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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: Heterodimer composed of formate dehydrogenase molybdopterin-binding subunit FdhA and 4Fe-4S dicluster domain-containing protein
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.122 MDa / Experimental value: NO
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Source (recombinant)Organism: Shewanella oneidensis MR-1 (bacteria)
Buffer solutionpH: 8 / Details: 0.1 M Tris-HCl, 0.1 M NaCl
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138699 / Symmetry type: POINT

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