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- EMDB-62562: Cryo-EM structure of reduced form of formate dehydrogenase from R... -

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Entry
Database: EMDB / ID: EMD-62562
TitleCryo-EM structure of reduced form of formate dehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH
Map data
Sample
  • Complex: Formate dehydrogenase from Rhodobacter aestuarii
    • Protein or peptide: formate dehydrogenase
    • Protein or peptide: Formate dehydrogenase delta subunit
    • Protein or peptide: Formate dehydrogenase gamma subunit
    • Protein or peptide: Formate dehydrogenase beta subunit
  • 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: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 1,4-DIHYDRONICOTINAMIDE 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 / 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 / Aspartate decarboxylase-like domain superfamily / : / 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 / 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: 3.09 Å
AuthorsZhang K / Zhang L
Funding support China, 1 items
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, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62562.png

Downloads & links

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Map

FileDownload / File: emd_62562.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-0.430834 - 1.7755373
Average (Standard dev.)0.0024203006 (±0.03697451)
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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Half map: #2

Fileemd_62562_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62562_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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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
    • Protein or peptide: Formate dehydrogenase delta subunit
    • Protein or peptide: Formate dehydrogenase gamma subunit
    • Protein or peptide: Formate dehydrogenase beta subunit
  • 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: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: 1,4-DIHYDRONICOTINAMIDE 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

MacromoleculeName: formate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Molecular weightTheoretical: 103.88007 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 AARRIEAAE

UniProtKB: Formate dehydrogenase alpha subunit

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Macromolecule #2: Formate dehydrogenase delta subunit

MacromoleculeName: Formate dehydrogenase delta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
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 #3: Formate dehydrogenase gamma subunit

MacromoleculeName: Formate dehydrogenase gamma subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter aestuarii (bacteria)
Molecular weightTheoretical: 15.814247 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
MTDLARLRAI LTAHEGREGA LLPILHDVQA DYGHIPDAAL EPIAKALRLS RAEVAGVVGF YHDFRRSPAG KHVIKLCRAE ACQAMGGDG VQARLEAALG LKLGETKHDI TLEAAYCLGL CACAPAAMVN DALVGRLDDA AVDTIAAEVR A

UniProtKB: Formate dehydrogenase gamma 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: 53.071684 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 PVLREAAE

UniProtKB: Formate dehydrogenase beta subunit

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Macromolecule #5: 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: 5 / 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 #6: MOLYBDENUM(VI) ION

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

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Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 7 / 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 #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: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 9 / Number of copies: 2 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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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 NaNO3, 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 overexpression in Escherichia coli MC1061 and purified using His-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: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 294386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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