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- EMDB-30995: Dehydrogenase holoenzyme -

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Basic information

Entry
Database: EMDB / ID: EMD-30995
TitleDehydrogenase holoenzyme
Map dataA combined map of MeFDH1 holoenzyme and MeFDH1_aN_b after sharpening
Sample
  • Complex: Formate dehydrogenase from Methylobacterium extorquens AM1 (MeFDH1)
    • Complex: Formate dehydrogenase alpha subunit from Methylobacterium extorquens AM1 (MeFDH1)
      • Protein or peptide: Formate dehydrogenase
    • Complex: Formate dehydrogenase beta subunit 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
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) / Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRoh SH / Park JS / Heo YY
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015M3D3A1A01064919 Korea, Republic Of
CitationJournal: To Be Published
Title: Dehydrogenase holoenzyme
Authors: Roh SH / Park JS
History
DepositionFeb 21, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7e5z
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30995.png

Downloads & links

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Map

FileDownload / File: emd_30995.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA combined map of MeFDH1 holoenzyme and MeFDH1_aN_b after sharpening
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.164 / Movie #1: 0.2
Minimum - Maximum-0.3920051 - 1.6048807
Average (Standard dev.)0.0073969266 (±0.034149624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 199.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z199.200199.200199.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.3921.6050.007

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Supplemental data

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Additional map: An electron density map of MeFDH1 aN b holoenzyme after sharpening

Fileemd_30995_additional_1.map
AnnotationAn electron density map of MeFDH1_aN_b holoenzyme after sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A combined map of MeFDH1 holoenzyme and MeFDH1 aN b

Fileemd_30995_additional_2.map
AnnotationA combined map of MeFDH1 holoenzyme and MeFDH1_aN_b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: An electron density map of MeFDH1 holoenzyme

Fileemd_30995_additional_3.map
AnnotationAn electron density map of MeFDH1 holoenzyme
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: An electron density map of MeFDH1 holoenzyme after sharpening

Fileemd_30995_additional_4.map
AnnotationAn electron density map of MeFDH1 holoenzyme after sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: An electron density map of MeFDH1 aN b holoenzyme after sharpening

Fileemd_30995_additional_5.map
AnnotationAn electron density map of MeFDH1_aN_b holoenzyme after sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: a half map of MeFDH1 aN b (only one set...

Fileemd_30995_additional_6.map
Annotationa half map of MeFDH1_aN_b (only one set of half maps could be uploaded so rest half maps were uploaded as additional EM maps with a corresponding FSC curve)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: a half map of MeFDH1 aN b (only one set...

Fileemd_30995_additional_7.map
Annotationa half map of MeFDH1_aN_b (only one set of half maps could be uploaded so rest half maps were uploaded as additional EM maps with a corresponding FSC curve)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: a half map of MeFDH1 holoenzyme

Fileemd_30995_half_map_1.map
Annotationa half map of MeFDH1 holoenzyme
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: a half map of MeFDH1 holoenzyme

Fileemd_30995_half_map_2.map
Annotationa half map of MeFDH1 holoenzyme
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 from Methylobacterium extorquens AM1 (MeFDH1)

EntireName: Formate dehydrogenase from Methylobacterium extorquens AM1 (MeFDH1)
Components
  • Complex: Formate dehydrogenase from Methylobacterium extorquens AM1 (MeFDH1)
    • Complex: Formate dehydrogenase alpha subunit from Methylobacterium extorquens AM1 (MeFDH1)
      • Protein or peptide: Formate dehydrogenase
    • Complex: Formate dehydrogenase beta subunit 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 from Methylobacterium extorquens AM1 (MeFDH1)

SupramoleculeName: Formate dehydrogenase from Methylobacterium extorquens AM1 (MeFDH1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methylorubrum extorquens AM1 (bacteria)
Recombinant expressionOrganism: Methylorubrum extorquens AM1 (bacteria)
Molecular weightExperimental: 70 KDa

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Supramolecule #2: Formate dehydrogenase alpha subunit from Methylobacterium extorqu...

SupramoleculeName: Formate dehydrogenase alpha subunit from Methylobacterium extorquens AM1 (MeFDH1)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Methylorubrum extorquens AM1 (bacteria)
Recombinant expressionOrganism: Methylorubrum extorquens AM1 (bacteria)

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Supramolecule #3: Formate dehydrogenase beta subunit from Methylobacterium extorque...

SupramoleculeName: Formate dehydrogenase beta subunit 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 (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / 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

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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 (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / 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

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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: 6.4
Component:
ConcentrationFormulaName
50.0 mMNa2HPO4sodium phosphate
100.0 mMNaclSodium chloridesodium chloride
2.0 mMC4H10O2S2Dithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV
Details: Blot time was for 4 seconds with 0 blot force before plunging..
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.1 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 100000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 2683 / Average exposure time: 3.0 sec. / Average electron dose: 50.0 e/Å2 / Details: Images were collected in movie-mode at
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1471548 / Details: Topaz picking facilitated particle picking
Startup modelType of model: INSILICO MODEL
In silico model: The startup model was generated by cryoSPARC ab initio processing.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 260910
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6tga

DetailsA initial model was from SWISS modeling using 6TGA as a template. Initial local fitting was done using Chimera and then ISOLDE plugged in ChimeraX for flexible fitting. The model was refined by using Phenix and Coot.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-7e5z:
Dehydrogenase holoenzyme

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