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- EMDB-33402: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33402
TitleFormate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
Map dataA auto-sharpened cryo EM map of MeFDH1
Sample
  • Complex: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
    • Complex: Alpha subunit of formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
      • Protein or peptide: Formate dehydrogenase
    • Complex: Beta subunit of formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
      • Protein or peptide: Tungsten-containing formate dehydrogenase beta subunit
  • Ligand: TUNGSTEN ION
  • 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: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FLAVIN MONONUCLEOTIDE
KeywordsElectron transport / oxidoreductase
Function / homology
Function and homology information


formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase complex / cellular respiration / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding ...formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase complex / cellular respiration / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding
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 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand 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 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain / SLBB domain / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Aspartate decarboxylase-like domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / 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 / formate dehydrogenase
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsPark J / Heo YY / Roh SH / Lee HH
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021M3A9I4021220 Korea, Republic Of
National Research Foundation (NRF, Korea)2019M3E5D6063871 Korea, Republic Of
CitationJournal: To Be Published
Title: Enzymatic conversion of CO2 in real flue gas to molar-scale formate
Authors: Jeon BW / Heo YY / Park J / Roh SH / Lee HH / Kim YH
History
DepositionMay 9, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33402.png

Downloads & links

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Map

FileDownload / File: emd_33402.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA auto-sharpened cryo EM map of MeFDH1
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 2.07
Minimum - Maximum-13.107659 - 17.905221999999998
Average (Standard dev.)-0.0038935377 (±0.41625354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: A density modified map of MeFDH1 from Phenix Resolve EM

Fileemd_33402_additional_1.map
AnnotationA density modified map of MeFDH1 from Phenix Resolve EM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map of MeFDH1

Fileemd_33402_half_map_1.map
AnnotationA half map of MeFDH1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map of MeFDH1

Fileemd_33402_half_map_2.map
AnnotationA half map of MeFDH1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 ...

EntireName: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
Components
  • Complex: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
    • Complex: Alpha subunit of formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
      • Protein or peptide: Formate dehydrogenase
    • Complex: Beta subunit of formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
      • Protein or peptide: Tungsten-containing formate dehydrogenase beta subunit
  • Ligand: TUNGSTEN ION
  • 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: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 ...

SupramoleculeName: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methylorubrum extorquens AM1 (bacteria)
Molecular weightTheoretical: 160 KDa

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Supramolecule #2: Alpha subunit of formate dehydrogenase (FDH) from Methylobacteriu...

SupramoleculeName: Alpha subunit of formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Methylorubrum extorquens AM1 (bacteria)

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Supramolecule #3: Beta subunit of formate dehydrogenase (FDH) from Methylobacterium...

SupramoleculeName: Beta subunit of formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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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: 108.292891 KDa
Recombinant expressionOrganism: Methylorubrum extorquens AM1 (bacteria)
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 EHHHHHH

UniProtKB: formate dehydrogenase

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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
Recombinant expressionOrganism: Methylorubrum extorquens AM1 (bacteria)
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: TUNGSTEN ION

MacromoleculeName: TUNGSTEN ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: W
Molecular weightTheoretical: 183.84 Da

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Macromolecule #4: 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: 4 / 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 #5: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 4 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #7: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / 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

Concentration0.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1761 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2

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Image processing

Particle selectionNumber selected: 2188878
Startup modelType of model: EMDB MAP
EMDB ID:

30995

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationNumber classes: 4 / Avg.num./class: 160000 / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 453262
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7e5z

RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 136.6
Output model

PDB-7xqw:
Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)

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