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- EMDB-32151: Cryo-EM Structure of Formate Dehydrogenase 1 from Methylorubrum e... -

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Basic information

Entry
Database: EMDB / ID: EMD-32151
TitleCryo-EM Structure of Formate Dehydrogenase 1 from Methylorubrum extorquens AM1
Map data
Sample
  • Complex: Formate Dehydrogenase 1 from Methylorubrum extorquens AM1
    • Protein or peptide: Formate dehydrogenase
    • Protein or peptide: Tungsten-containing formate dehydrogenase beta subunit
  • Ligand: IRON/SULFUR CLUSTER
  • 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: TUNGSTEN ION
  • Ligand: UNKNOWN ATOM OR ION
  • Ligand: FLAVIN MONONUCLEOTIDE
KeywordsComplex / OXIDOREDUCTASE
Function / homology
Function and homology information


formate metabolic process / formate dehydrogenase / 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 ...formate metabolic process / formate dehydrogenase / 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 / metal ion binding / membrane
Similarity search - Function
Formate dehydrogenase H, molybdopterin-binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Soluble ligand binding domain / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain ...Formate dehydrogenase H, molybdopterin-binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Soluble ligand binding domain / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / 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
Tungsten-containing formate dehydrogenase beta subunit / Tungsten-containing formate dehydrogenase alpha subunit
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsYoshikawa T / Makino F / Miyata T / Suzuki Y / Tanaka H / Namba K / Sowa K / Kitazumi Y / Shirai O
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Society for the Promotion of Science (JSPS)JP21H01961 Japan
CitationJournal: Chem Commun (Camb) / Year: 2022
Title: Multiple electron transfer pathways of tungsten-containing formate dehydrogenase in direct electron transfer-type bioelectrocatalysis.
Authors: Tatsushi Yoshikawa / Fumiaki Makino / Tomoko Miyata / Yohei Suzuki / Hideaki Tanaka / Keiichi Namba / Kenji Kano / Keisei Sowa / Yuki Kitazumi / Osamu Shirai /
Abstract: Tungsten-containing formate dehydrogenase from AM1 (FoDH1)-a promising biocatalyst for the interconversion of carbon dioxide/formate and nicotine adenine dinucleotide (NAD)/NADH redox couples-was ...Tungsten-containing formate dehydrogenase from AM1 (FoDH1)-a promising biocatalyst for the interconversion of carbon dioxide/formate and nicotine adenine dinucleotide (NAD)/NADH redox couples-was investigated using structural biology and bioelectrochemistry. FoDH1 is reported to be an enzyme that can realize "direct electron transfer (DET)-type bioelectrocatalysis." However, its 3-D structure, electrode-active sites, and electron transfer (ET) pathways remain unclear. The ET pathways were investigated using structural information, electrostatic interactions between the electrode and the enzyme, and the differences in the substrates. Two electrode-active sites and multiple ET pathways in FoDH1 were discovered.
History
DepositionNov 9, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32151.png

Downloads & links

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Map

FileDownload / File: emd_32151.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.113699876 - 0.3838
Average (Standard dev.)0.00010581136 (±0.0071058953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Formate Dehydrogenase 1 from Methylorubrum extorquens AM1

EntireName: Formate Dehydrogenase 1 from Methylorubrum extorquens AM1
Components
  • Complex: Formate Dehydrogenase 1 from Methylorubrum extorquens AM1
    • Protein or peptide: Formate dehydrogenase
    • Protein or peptide: Tungsten-containing formate dehydrogenase beta subunit
  • Ligand: IRON/SULFUR CLUSTER
  • 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: TUNGSTEN ION
  • Ligand: UNKNOWN ATOM OR ION
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Formate Dehydrogenase 1 from Methylorubrum extorquens AM1

SupramoleculeName: Formate Dehydrogenase 1 from Methylorubrum extorquens AM1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Soluble Heterodimer
Source (natural)Organism: Methylorubrum extorquens AM1 (bacteria)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: Formate dehydrogenase

MacromoleculeName: Formate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Methylorubrum extorquens AM1 (bacteria) / Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1
Molecular weightTheoretical: 107.464 KDa
SequenceString: MSNGPEPHGN KIEQPEIRAD ERQDAGGPAN GAPSTSGGAY SQGAKSGGQA APDPSGSYGI KDAPVAPATI AFEFDGQQVE AQPGETIWA VAKRLGTHIP HLCHKPDPGY RPDGNCRACM VEIEGERVLA ASCKRTPAIG MKVKSATERA TKARAMVLEL L VADQPERA ...String:
MSNGPEPHGN KIEQPEIRAD ERQDAGGPAN GAPSTSGGAY SQGAKSGGQA APDPSGSYGI KDAPVAPATI AFEFDGQQVE AQPGETIWA VAKRLGTHIP HLCHKPDPGY RPDGNCRACM VEIEGERVLA ASCKRTPAIG MKVKSATERA TKARAMVLEL L VADQPERA TSHDPSSHFW VQADVLDVTE SRFPAAERWT SDVSHPAMSV NLDACIQCNL CVRACREVQV NDVIGMAYRA AG SKVVFDF DDPMGGSTCV ACGECVQACP TGALMPAAYL DANQTRTVYP DREVKSLCPY CGVGCQVSYK VKDERIVYAE GVN GPANQN RLCVKGRFGF DYVHHPHRLT VPLIRLENVP KDANDQVDPA NPWTHFREAT WEEALDRAAG GLKAIRDTNG RKAL AGFGS AKGSNEEAYL FQKLVRLGFG TNNVDHCTRL CHASSVAALM EGLNSGAVTA PFSAALDAEV IVVIGANPTV NHPVA ATFL KNAVKQRGAK LIIMDPRRQT LSRHAYRHLA FRPGSDVAML NAMLNVIVTE GLYDEQYIAG YTENFEALRE KIVDFT PEK MASVCGIDAE TLREVARLYA RAKSSLIFWG MGVSQHVHGT DNSRCLIALA LITGQIGRPG TGLHPLRGQN NVQGASD AG LIPMVYPDYQ SVEKDAVREL FEEFWGQSLD PQKGLTVVEI MRAIHAGEIR GMFVEGENPA MSDPDLNHAR HALAMLDH L VVQDLFLTET AFHADVVLPA SAFAEKAGTF TNTDRRVQIA QPVVAPPGDA RQDWWIIQEL ARRLDLDWNY GGPADIFAE MAQVMPSLNN ITWERLEREG AVTYPVDAPD QPGNEIIFYA GFPTESGRAK IVPAAIVPPD EVPDDEFPMV LSTGRVLEHW HTGSMTRRA GVLDALEPEA VAFMAPKELY RLGLRPGGSM RLETRRGAVV LKVRSDRDVP IGMIFMPFCY AEAAANLLTN P ALDPLGKI PEFKFCAARV VPAEAAPMAA E

UniProtKB: Tungsten-containing formate dehydrogenase alpha subunit

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Macromolecule #2: Tungsten-containing formate dehydrogenase beta subunit

MacromoleculeName: Tungsten-containing formate dehydrogenase beta subunit
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Methylorubrum extorquens AM1 (bacteria) / Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1
Molecular weightTheoretical: 62.397508 KDa
SequenceString: MSEASGTVRS FAHPGRGRNV ARAVPKGRQV DPHAKVEIEE LLGTRPRQRD LLIEHLHLIQ DTYGQISADH LAALADEMSL AFAEVFETA TFYAHFDVVK EGEADIPRLT IRVCDSITCA MFGADELLET LQRELASDAV RVVRAPCVGL CDHAPAVEVG H NFLHRADL ...String:
MSEASGTVRS FAHPGRGRNV ARAVPKGRQV DPHAKVEIEE LLGTRPRQRD LLIEHLHLIQ DTYGQISADH LAALADEMSL AFAEVFETA TFYAHFDVVK EGEADIPRLT IRVCDSITCA MFGADELLET LQRELASDAV RVVRAPCVGL CDHAPAVEVG H NFLHRADL ASVRAAVEAE DTHAHIPTYV DYDAYRAGGG YATLERLRSG ELPVDDVLKV LDDGGLRGLG GAGFPTGRKW RS VRGEPGP RLMAVNGDEG EPGTFKDQLY LNTDPHRFLE GMLIGAHVVE AADVYIYLRD EYPISREILA REIAKLPEGG TRI HLRRGA GAYICGEESS LIESLEGKRG LPRHKPPFPF QVGLFNRPTL INNIETLFWV RDLIERGAEW WKSHGRNGRV GLRS YSVSG RVKEPGVKLA PAGLTIQELI DEYCGGISDG HSFAAYLPGG ASGGILPASM NDIPLDFGTL EKYGCFIGSA AVVIL SDQD DVRGAALNLM KFFEDESCGQ CTPCRSGTQK ARMLMENGVW DTDLLGELAQ CMRDASICGL GQAASNPVST VIKYFP DLF PEPRAVAAE

UniProtKB: Tungsten-containing formate dehydrogenase beta subunit

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Macromolecule #3: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 3 / Number of copies: 4 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #4: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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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: 2 / 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: TUNGSTEN ION

MacromoleculeName: TUNGSTEN ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: W
Molecular weightTheoretical: 183.84 Da

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Macromolecule #7: UNKNOWN ATOM OR ION

MacromoleculeName: UNKNOWN ATOM OR ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: UNX

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Macromolecule #8: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 8 / Number of copies: 1 / 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

Concentration5 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
20.0 mMKH2PO4Potassium dihydrogenphosphate
20.0 mMK2HPO4dipotassium hydrogenphosphate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7650 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsC2 aperture diameter: 40.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 57471 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1594212
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 289653
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 142600 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7vw6:
Cryo-EM Structure of Formate Dehydrogenase 1 from Methylorubrum extorquens AM1

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