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- PDB-9ktr: Cryo-EM structure of formate dehydrogenase from Rhodobacter aestu... -

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Basic information

Entry
Database: PDB / ID: 9ktr
TitleCryo-EM structure of formate dehydrogenase from Rhodobacter aestuarii (RaFDH) with NAD+
Components
  • (Formate dehydrogenase ...) x 3
  • formate dehydrogenase
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 / metal ion binding / membrane
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 / Aspartate decarboxylase-like domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / 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
GUANYLATE-O'-PHOSPHORIC ACID / : / 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: 2.55 Å
AuthorsZhang, K. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDC0120103 China
CitationJournal: To Be Published
Title: Mechanistic understanding on the catalytic preference of formate dehydrogenase from Rhodobacter aestuarii towards carbon dioxide reduction
Authors: Zhang, K. / Zhang, L.
History
DepositionDec 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 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: formate dehydrogenase
G: Formate dehydrogenase delta subunit
F: Formate dehydrogenase gamma subunit
H: Formate dehydrogenase delta subunit
C: Formate dehydrogenase beta subunit
E: Formate dehydrogenase gamma subunit
B: formate dehydrogenase
D: Formate dehydrogenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,50832
Polymers359,8928
Non-polymers9,61524
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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Protein , 1 types, 2 molecules AB

#1: Protein formate dehydrogenase


Mass: 103880.070 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, formate dehydrogenase

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Formate dehydrogenase ... , 3 types, 6 molecules GHFECD

#2: Protein Formate dehydrogenase delta subunit


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


Mass: 15814.247 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
#4: Protein Formate dehydrogenase beta subunit


Mass: 53071.684 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 , 7 types, 24 molecules

#5: Chemical ChemComp-2MD / GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER / MOLYBDENUM COFACTOR,BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE)


Mass: 742.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N10O13P2S2 / 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.: 3 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#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-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.: 10 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#10: 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
#11: 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 modificationY

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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: 0.359388 MDa / Experimental value: NO
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Source (recombinant)Organism: Escherichia coli MC1061 (bacteria)
Buffer solutionpH: 7.5 / Details: 10mM NaNO3, 100mM PBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The protein was obtained after overexpression in Escherichia coli MC1061 and purified using His-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
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156156 / Symmetry type: POINT
Atomic model buildingSource name: SwissModel / Type: in silico model
RefinementHighest resolution: 2.55 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_d0.56535462
ELECTRON MICROSCOPYf_dihedral_angle_d10.3554051
ELECTRON MICROSCOPYf_chiral_restr0.0413976
ELECTRON MICROSCOPYf_plane_restr0.0054616

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