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- PDB-9wxb: Cryo-EM structure of reduced form of formatedehydrogenase from Rh... -

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Basic information

Entry
Database: PDB / ID: 9wxb
TitleCryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH
Components(Formate dehydrogenase ...) x 4
KeywordsOXIDOREDUCTASE / formate dehydrogenase / formate oxidation / carbon dioxide redcution / FMN / NAD
Function / homology
Function and homology information


formate metabolic process / formate dehydrogenase (NAD+) activity / oxidoreductase complex / molybdopterin cofactor binding / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding ...formate metabolic process / formate dehydrogenase (NAD+) activity / oxidoreductase complex / molybdopterin cofactor binding / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding
Similarity search - Function
Formate dehydrogenase, delta subunit / NADH-dependant formate dehydrogenase delta subunit FdsD / NADP-reducing hydrogenase subunit HndA / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain ...Formate dehydrogenase, delta subunit / NADH-dependant formate dehydrogenase delta subunit FdsD / NADP-reducing hydrogenase subunit HndA / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / 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 / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Aspartate decarboxylase-like domain superfamily / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-MGD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / IRON/SULFUR CLUSTER / Formate dehydrogenase delta subunit / Formate dehydrogenase alpha subunit / Formate dehydrogenase beta subunit / Formate dehydrogenase gamma subunit
Similarity search - Component
Biological speciesRhodobacter aestuarii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang, K. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDC0120103 China
CitationJournal: Adv Sci (Weinh) / Year: 2026
Title: Understanding the Catalytic Determinant role of Diaphorase-Like Subunit in Formate Dehydrogenases via Redox Couples.
Authors: Kuncheng Zhang / Weisong Liu / Hao Su / Huijuan Cui / Yuanming Wang / Zhiguang Zhu / Chun You / Lingling Zhang /
Abstract: Multi-subunit formate dehydrogenases (FDHs), which catalyze the interconversion of formate and carbon dioxide (CO), have drawn increasing attention for mitigating climate change and advancing ...Multi-subunit formate dehydrogenases (FDHs), which catalyze the interconversion of formate and carbon dioxide (CO), have drawn increasing attention for mitigating climate change and advancing environmental protection owing to their advantages of oxygen tolerance and easy heterogenous expression. However, differently sourced multi-subunit FDHs exhibit distinct catalytic biases, and the reasons remain unclear. On the basis of the exceptional observation of Rhodobacter aestuarii FDH favoring CO reduction, this study unveiled an oxidation inhibition effect in exclusively NADH/NAD-involved catalysis via kinetics analysis in terms of different redox couples. Substrate truncation positioned Fdhβ as the predominant subunit. Further studies based on structural and electrochemical insights interpreted that the slow desorption of NADH is the underlying determinant for the apparent catalytic bias. Knowledge-based rational design helped obtain a beneficial variant, RaFDH β E260Y, with a 10-fold increased catalytic activity in CO reduction, highlighting its potential for CO biotransformation and applications in low-carbon biomanufacturing. Eventually, bioinformatic analysis suggested that the diaphorase-like subunits and the catalysis regulation mechanism may widely exist in living organisms for modulating the redox balance of oxidoreductases, providing new insights into metabolism and catabolism.
History
DepositionSep 25, 2025Deposition site: PDBJ / Processing site: PDBC
SupersessionJun 3, 2026ID: 9KTL, 9KTR
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 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

Downloads & links

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Assembly

Deposited unit
G: Formate dehydrogenase delta subunit
E: Formate dehydrogenase gamma subunit
B: Formate dehydrogenase alpha subunit
H: Formate dehydrogenase delta subunit
C: Formate dehydrogenase beta subunit
A: Formate dehydrogenase alpha subunit
F: Formate dehydrogenase gamma subunit
D: Formate dehydrogenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)376,02332
Polymers366,4098
Non-polymers9,61324
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Formate dehydrogenase ... , 4 types, 8 molecules GHEFBACD

#1: Protein Formate dehydrogenase delta subunit


Mass: 7180.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter aestuarii (bacteria) / Gene: SAMN05421580_102355 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A1N7KD80, formate dehydrogenase
#2: Protein Formate dehydrogenase gamma subunit


Mass: 19331.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter aestuarii (bacteria) / Gene: SAMN05421580_102359 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A1N7KDI2
#3: Protein Formate dehydrogenase alpha subunit


Mass: 103750.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter aestuarii (bacteria) / Gene: SAMN05421580_102357 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A1N7KDD5
#4: Protein Formate dehydrogenase beta subunit


Mass: 52942.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter aestuarii (bacteria) / Gene: SAMN05421580_102358 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A1N7KDE1

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Non-polymers , 6 types, 24 molecules

#5: 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
#6: 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.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#10: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / 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: Formate dehydrogenase from Rhodobacter aestuarii / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.359 MDa / Experimental value: NO
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Source (recombinant)Organism: Escherichia coli MC1061 (bacteria)
Buffer solutionpH: 7.5 / Details: 10mM NaN03, 100mM PBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The protein was obtained after overexpressionin Escherichia coli MC106l and purified usingHis-tagged nickel affinity chromatography and size-exclusion chromatography.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1CTFFINDparticle selection
2PHENIX1.20.1_4487model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192652 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325964
ELECTRON MICROSCOPYf_angle_d0.48535462
ELECTRON MICROSCOPYf_dihedral_angle_d8.6834011
ELECTRON MICROSCOPYf_chiral_restr0.043976
ELECTRON MICROSCOPYf_plane_restr0.0044616

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