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- EMDB-66342: Cryo-EM structure of reduced form of formatedehydrogenase from Rh... -

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Entry
Database: EMDB / ID: EMD-66342
TitleCryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH
Map data
Sample
  • Complex: Formate dehydrogenase from Rhodobacter aestuarii
    • Protein or peptide: Formate dehydrogenase delta subunit
    • Protein or peptide: Formate dehydrogenase gamma subunit
    • Protein or peptide: Formate dehydrogenase alpha subunit
    • Protein or peptide: Formate dehydrogenase beta subunit
  • Ligand: FE2/S2 (INORGANIC) 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(VI) ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: FLAVIN MONONUCLEOTIDE
Keywordsformate dehydrogenase / formate oxidation / carbon dioxide redcution / FMN / NAD / OXIDOREDUCTASE
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
Formate dehydrogenase delta subunit / Formate dehydrogenase alpha subunit / Formate dehydrogenase beta subunit / Formate dehydrogenase gamma subunit
Similarity search - Component
Biological speciesRhodobacter aestuarii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang K / Zhang L
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66342.png

Downloads & links

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Map

FileDownload / File: emd_66342.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.151
Minimum - Maximum-0.5914264 - 2.364865
Average (Standard dev.)0.0032049988 (±0.047958117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_66342_additional_1.map
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Half map: #2

Fileemd_66342_half_map_1.map
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Half map: #1

Fileemd_66342_half_map_2.map
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Sample components

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Entire : Formate dehydrogenase from Rhodobacter aestuarii

EntireName: Formate dehydrogenase from Rhodobacter aestuarii
Components
  • Complex: Formate dehydrogenase from Rhodobacter aestuarii
    • Protein or peptide: Formate dehydrogenase delta subunit
    • Protein or peptide: Formate dehydrogenase gamma subunit
    • Protein or peptide: Formate dehydrogenase alpha subunit
    • Protein or peptide: Formate dehydrogenase beta subunit
  • Ligand: FE2/S2 (INORGANIC) 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(VI) ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Formate dehydrogenase from Rhodobacter aestuarii

SupramoleculeName: Formate dehydrogenase from Rhodobacter aestuarii / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Molecular weightTheoretical: 359 KDa

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Macromolecule #1: Formate dehydrogenase delta subunit

MacromoleculeName: Formate dehydrogenase delta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Molecular weightTheoretical: 7.180213 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
MSDEKLIRMA NQIAAFFAVQ PADRAEGVAA HISDNWAAPM RAALLAHIAA GGAGLDALVV DAAPHIRPAG

UniProtKB: Formate dehydrogenase delta subunit

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Macromolecule #2: Formate dehydrogenase gamma subunit

MacromoleculeName: Formate dehydrogenase gamma subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Molecular weightTheoretical: 19.331008 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
SRAWRHPQGG SHHHHHHGMR DLYDDDDKHM TDLARLRAIL TAHEGREGAL LPILHDVQAD YGHIPDAALE PIAKALRLSR AEVAGVVGF YHDFRRSPAG KHVIKLCRAE ACQAMGGDGV QARLEAALGL KLGETKHDIT LEAAYCLGLC ACAPAAMVND A LVGRLDDA AVDTIAAEVR A

UniProtKB: Formate dehydrogenase gamma subunit

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Macromolecule #3: Formate dehydrogenase alpha subunit

MacromoleculeName: Formate dehydrogenase alpha subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Molecular weightTheoretical: 103.750953 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString: MKDLIIPPLD WTQDMGTPAR HGAPVTLTVD GVEVTVPAGT SVLRAAAQAG ISIPKLCATD SVEPVGSCRL CMVEIEGMRG MPSSCTTPV AAGMQVHTQT PQLQKLRRGV MELYISDHPL DCLTCAANGD CELQDMAGAV GLREVRYTKG ENHFEVRQGG E ANPCYIPK ...String:
MKDLIIPPLD WTQDMGTPAR HGAPVTLTVD GVEVTVPAGT SVLRAAAQAG ISIPKLCATD SVEPVGSCRL CMVEIEGMRG MPSSCTTPV AAGMQVHTQT PQLQKLRRGV MELYISDHPL DCLTCAANGD CELQDMAGAV GLREVRYTKG ENHFEVRQGG E ANPCYIPK DTSNPYFSYD PAKCIVCMRC VRACEEVQGT FALTVDGRGF EARISPAADN FLASDCVSCG ACVQACPTAT LV EKSVEEI GTPERKVVTT CAYCGVGCSF EAHMRGEELV RMVPWKGGAA NRGHSCVKGR FAYGYATHRD RILKPMIREK VSD PWREVS WEEALGFTAA RLNAARATHG ADALGVITSS RCTNEETYLV QKLARAVFGT NNTDTCARVC HSPTGYGLKQ TFGT SAGTQ DFDSVEDTDL ALVIGANPTD GHPVFASRLR KRLRAGAKLI VVDPRRIDLL ETPHIGDSWH LPLRPGTNVA VLVAL AHVI VTEKLYDAAF ISERCDGDEW ADYAEFVSNP EYAPEAVESL TGVPADTLRE AARAYAAAPN AAIYYGLGVT EHSQGS TTV IAIANLAMMT GNIGRPGVGV NPLRGQNNVQ GSCDMGSFPH ELPGYRHVAD DAARSLFEKA WGVALSSEPG LRIPNML DA AVAGQFKALY VQGEDILQSD PDTRHVAAGL AAMDLVIVHD LFLNETANYA HVFLPGSSFL EKDGTFTNAE RRINRVRR V MRPKNGYADW EVTQLLANAL GAGWAYTHPR EIMAEIAATT PGFANVTYEM LDARGSVQWP CNEAAPEGSP IMHVDGFVR GKGRFIRTAY LPTDERTGPR FPLLLTTGRI LSQYNVGAQT RRTENVAWHA EDRLEIHPTD AENRGIREGD WVRVASRAGE TTLRATVTD RVSPGVVYTT FHHPDTQANV VTTDNSDWAT NCPEYKVTAV QVAPSNGPSA WQEDYTAQAT AARRIEAA

UniProtKB: Formate dehydrogenase alpha subunit

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Macromolecule #4: Formate dehydrogenase beta subunit

MacromoleculeName: Formate dehydrogenase beta subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Molecular weightTheoretical: 52.942566 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString: MKIWVPCDAA AKACGAERVV AEITAQAAAR GVSVDIRRNG TRGMVWLEPL VEVETEAGRV GFGPMTPADV PALFEDLAAH PKALGLVEE IPFFKRQTRL TFARCGRNEP LCLDQYETTG GWDGLRKALA MTPAEVVEEI ISSGLRGRGG AGFPTGIKWR T VLGAAADQ ...String:
MKIWVPCDAA AKACGAERVV AEITAQAAAR GVSVDIRRNG TRGMVWLEPL VEVETEAGRV GFGPMTPADV PALFEDLAAH PKALGLVEE IPFFKRQTRL TFARCGRNEP LCLDQYETTG GWDGLRKALA MTPAEVVEEI ISSGLRGRGG AGFPTGIKWR T VLGAAADQ KYIVCNVDEG DSGSFADRML IEGDPFCLIE GMAVAGHAVG ATRGYVYIRS EYPDCISVMR AAIILAEQSG IL AEAGFSL EVRVGAGAYV CGEETAMLNS IEGKRGTVRP KPPLPALEGL FGKPTVVNNL LSLAAVPWIL AHGGAAYQSY GID RSRGTI PLQVGGNVKY GGLFETGFGI TLGELVMDVC GGTASGRPVK AVQVGGPLGA YHPQADFDLP FCYELFAGQG GLVG HAGLV VHDDRADMLK LARFAMEFCA VESCGTCTPC RIGAVRGVET LDRIAAGDAA ALPLLDDLCD TMKYGSLCAL GGFTP YPVQ SAIRHFPQDF PVLREAA

UniProtKB: Formate dehydrogenase beta subunit

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Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 5 / 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 #6: 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: 6 / Number of copies: 4 / 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 #7: MOLYBDENUM(VI) ION

MacromoleculeName: MOLYBDENUM(VI) ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: 6MO
Molecular weightTheoretical: 95.94 Da

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Macromolecule #8: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 8 / Number of copies: 10 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #9: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 9 / Number of copies: 2 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #10: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 10 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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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

Concentration1 mg/mL
BufferpH: 7.5 / Details: 10mM NaN03, 100mM PBS
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThe protein was obtained after overexpressionin Escherichia coli MC106l and purified usingHis-tagged nickel affinity chromatography and size-exclusion chromatography.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 5.0 µm / Nominal defocus min: 1.2 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 192652
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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