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- EMDB-19534: CryoEM structure of the Elp-Hdr complex of Methanothermobacter ma... -

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Basic information

Entry
Database: EMDB / ID: EMD-19534
TitleCryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2, dimer (composite structure)
Map dataComposite map of dimeric Elp-Hdr under conformational state 2
Sample
  • Complex: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
    • Protein or peptide: x 6 types
  • Ligand: x 5 types
KeywordsRedox / Flavin-based electron bifurcation / methanogenesis / heterodisulfide reductase / F420-H2 oxidase / Oxidoreductase
Function / homology
Function and homology information


formate dehydrogenase (coenzyme F420) / formate dehydrogenase (coenzyme F420) activity / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate dehydrogenase / methanogenesis / NADH dehydrogenase activity / iron-sulfur cluster binding / respiratory electron transport chain ...formate dehydrogenase (coenzyme F420) / formate dehydrogenase (coenzyme F420) activity / H2:CoB-CoM heterodisulfide,ferredoxin reductase / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate dehydrogenase / methanogenesis / NADH dehydrogenase activity / iron-sulfur cluster binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / membrane / plasma membrane
Similarity search - Function
F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal ...F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / 4Fe-4S dicluster domain / Alanine dehydrogenase/PNT, C-terminal domain / 4Fe-4S dicluster domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin / 4Fe-4S binding domain / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Methyl viologen-reducing hydrogenase, subunit D-related protein / formate dehydrogenase (coenzyme F420) / Formate dehydrogenase, alpha subunit / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSan Segundo-Acosta P / Murphy BJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nature / Year: 2025
Title: Electron flow in hydrogenotrophic methanogens under nickel limitation.
Authors: Shunsuke Nomura / Pablo San Segundo-Acosta / Evgenii Protasov / Masanori Kaneko / Jörg Kahnt / Bonnie J Murphy / Seigo Shima /
Abstract: Methanogenic archaea are the main producers of the potent greenhouse gas methane. In the methanogenic pathway from CO and H studied under laboratory conditions, low-potential electrons for CO ...Methanogenic archaea are the main producers of the potent greenhouse gas methane. In the methanogenic pathway from CO and H studied under laboratory conditions, low-potential electrons for CO reduction are generated by a flavin-based electron-bifurcation reaction catalysed by heterodisulfide reductase (Hdr) complexed with the associated [NiFe]-hydrogenase (Mvh). F-reducing [NiFe]-hydrogenase (Frh) provides electrons to the methanogenic pathway through the electron carrier F (ref. ). Here we report that under strictly nickel-limited conditions, in which the nickel concentration is similar to those often observed in natural habitats, the production of both [NiFe]-hydrogenases in Methanothermobacter marburgensis is strongly downregulated. The Frh reaction is substituted by a coupled reaction with [Fe]-hydrogenase (Hmd), and the role of Mvh is taken over by F-dependent electron-donating proteins (Elp). Thus, Hmd provides all electrons for the reducing metabolism under these nickel-limited conditions. Biochemical and structural characterization of Elp-Hdr complexes confirms the electronic interaction between Elp and Hdr. The conservation of the genes encoding Elp and Hmd in CO-reducing hydrogenotrophic methanogens suggests that the Hmd system is an alternative pathway for electron flow in CO-reducing hydrogenotrophic methanogens under nickel-limited conditions.
History
DepositionFeb 15, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19534.jpg

Downloads & links

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Map

FileDownload / File: emd_19534.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of dimeric Elp-Hdr under conformational state 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 448 pix.
= 374.976 Å		0.84 Å/pix.
x 448 pix.
= 374.976 Å		0.84 Å/pix.
x 448 pix.
= 374.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.6
Minimum - Maximum-23.19867 - 46.014698000000003
Average (Standard dev.)0.002630302 (±0.85482836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 374.976 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : F420-dependent electron-donating proteins- heterodisulfide reduct...

EntireName: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
Components
  • Complex: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
    • Protein or peptide: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
    • Protein or peptide: Formate dehydrogenase, alpha subunit
    • Protein or peptide: Formate dehydrogenase, beta subunit
    • Protein or peptide: Methyl viologen-reducing hydrogenase, subunit D-related protein
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: water

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Supramolecule #1: F420-dependent electron-donating proteins- heterodisulfide reduct...

SupramoleculeName: F420-dependent electron-donating proteins- heterodisulfide reductase complex (Elp-Hdr) from Methanothermobacter marburgensis (heterodisulfide reductase core and mobile arm, composite structure)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 70.412883 KDa
SequenceString: PKIGVYVCHC GVNIGGVVDV EAVRDYAAKL PNVVIAKDYK YYCSDPGQLE IQKDIKELGI NRVVVAACSP RLHEPTFRRC VEEAGLNQF LFEFANIREH DSWVHMDNPE GATEKAKDLV RMAVAKARLL EPLEASKVSV DDKALVIGGG VAGIQAALDL A DMGFKTYM ...String:
PKIGVYVCHC GVNIGGVVDV EAVRDYAAKL PNVVIAKDYK YYCSDPGQLE IQKDIKELGI NRVVVAACSP RLHEPTFRRC VEEAGLNQF LFEFANIREH DSWVHMDNPE GATEKAKDLV RMAVAKARLL EPLEASKVSV DDKALVIGGG VAGIQAALDL A DMGFKTYM VEKRPSISGR MGQLDKTFPT LDCSMCILAP KMVDVGKHDN IELITYAEVK EVDGYIGNFK VKIEKKPRYI DE ELCTGCG SCVEVCPIEM PNYFDEGIGM TKAVYIPFPQ AVPLCATIDK DYCIECMLCD EVCERGAVKH DQEPEEIEIE VGT IIVATG YDAYDPTEKL EYGYGRHTNV ITGLELERMI NASGPTDGKV LKPSDGEKPK RVAFIHCVGS RDEQIGKPYC SRVC CMYIM KNAQLIKDKM PDTEVTLYYM DIRAFGKGFE EFYKRSQEKY GIKFIRGRPA EVIENPDLTL TVRSEDTLLG KVTEY DYDM VVLGVGLVPP EGAETLRQTI GLSKSADGFL MEAHPKLRPV DTLTDGVYLA GVAQGPKDIP DAVAQASGAA ARAAIP MVK GEVEIEPIIA VTDSDVCGGC EVCIELCPFG AISIEEGHAN VNVALCKGCG TCVAACPSGA MDQQHFKTEQ IMAQIEA AL N

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A

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Macromolecule #2: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 31.538227 KDa
SequenceString: MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE ...String:
MEIAYFLGCI MNNRYPGIEK ATRVLFDKLG IELKDMEGAS CCPAPGVFGS FDKTTWAAIA ARNITIAEDM GADIMTECNG CFGSLFETN HLLKEDEEMK AKINEILKET GREYKGEVNV RHFAEVLYND VGLDKLSELV EKPLNLNVAV HYGCHFLKPS D EINIDNPE RPTILDEIVE VTGAKSVEYK DKMMCCGAGG GVRSRDLDVA LDFTREKLTN MKEAGVDAIV NVCPFCHLQF DV GQMEIKD KFGEEFDIPV LHLAQLLGLA MGLPKEDLVV DAHQVCV

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B

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Macromolecule #3: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

MacromoleculeName: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: H2:CoB-CoM heterodisulfide,ferredoxin reductase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 20.288418 KDa
SequenceString:
TLLQREENII RKGNIDKEFS EKIKAAGGDS LEYCFQCGTC TGSCPSGRRT PYRVRQIIRK ANVGLKDEII SDPTLWMCTT CYSCQERCP RKVKIVDVVK LARNEAAKAG FMAPAHKAVG SFVIKTGHGV PINDATMELR KAVGLGELPP TTHQFPEALE E VQKIIKAT GFDQLIGYNW ETGEL

UniProtKB: H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C

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Macromolecule #4: Formate dehydrogenase, alpha subunit

MacromoleculeName: Formate dehydrogenase, alpha subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 37.379363 KDa
SequenceString: MVKHTLCPSC SAGCGVNIVE MGGAPVGTYP YRRHPVNEGK TCRAGRDCYE IPLMDRVTSP GVKKSGKLSG VNWDEALDKL TELLSSEDI SILTTGTLTN EEALKLREII ENFNVKKSGL ITVFPEFDYP EIDIRNIRDY DNIAVIGDAI TCAPLIGRRI F HAMAAGAE ...String:
MVKHTLCPSC SAGCGVNIVE MGGAPVGTYP YRRHPVNEGK TCRAGRDCYE IPLMDRVTSP GVKKSGKLSG VNWDEALDKL TELLSSEDI SILTTGTLTN EEALKLREII ENFNVKKSGL ITVFPEFDYP EIDIRNIRDY DNIAVIGDAI TCAPLIGRRI F HAMAAGAE VRSYDRRDET RMAVNSGFHI TFSDEREVLN DLQQLPGGSL IIITPEIPEI IGPVLEFSSE NEFDVLPIFE DF NTRGVMQ HLPPVNEGEF DSVWLIDPGA AAEPVDVSGK FVLQSIRTEG LTPDIFLPVA AWCEKSGSYT STAGYTMKLE PAL QAPEGV LSDMEIFERI LRA

UniProtKB: Formate dehydrogenase, alpha subunit

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Macromolecule #5: Formate dehydrogenase, beta subunit

MacromoleculeName: Formate dehydrogenase, beta subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 43.387148 KDa
SequenceString: MKYLLARATD EEIQRKGECG GAVTAIFKYM LDKEVVDAVL TLERGYDVYD GIPVLLEDSS GIESTCGSLH CAPTMFGDLI SRYLSDMRL AVAVKPCDAM AIRELEKRHQ IDPDKVYKIG LNCGGTLAPV SAREMIETFY EIDPDDVVSE EIDRGKFIVE L RDGSHREI ...String:
MKYLLARATD EEIQRKGECG GAVTAIFKYM LDKEVVDAVL TLERGYDVYD GIPVLLEDSS GIESTCGSLH CAPTMFGDLI SRYLSDMRL AVAVKPCDAM AIRELEKRHQ IDPDKVYKIG LNCGGTLAPV SAREMIETFY EIDPDDVVSE EIDRGKFIVE L RDGSHREI SIDYLEEEGF GRRENCQRCE IMVPRNADLA CGNWGADDGW TFIEVNTERG QEIIEGARSS GYIEAREPSE KM VKIREKI ENAMISMARK FQDKYLDEEY PSLDEWDEYW KRCINCFACR DACPVCFCRE CELEKDYLLE SDEKAPDPLT FQG VRLSHM GFSCINCGQC EDVCPMDIPI ARIYHRIQKK YRDRTGFTAG VSQELPPMYS GEKD

UniProtKB: formate dehydrogenase (coenzyme F420)

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Macromolecule #6: Methyl viologen-reducing hydrogenase, subunit D-related protein

MacromoleculeName: Methyl viologen-reducing hydrogenase, subunit D-related protein
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Molecular weightTheoretical: 14.788889 KDa
SequenceString:
FEPKIVGFCC NWCSYGGADT AGTARMQYPP NVRIIRVMCS GRVNASMILK AFSEGADGVF VGGCHIGDCH YDSGNYKWKR RARFIEDIL PEFGIDKERF RWEWISASEG EKFQKTMQEF YETVKYLGPL

UniProtKB: Methyl viologen-reducing hydrogenase, subunit D-related protein

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 13 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #8: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 8 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #9: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 9 / Number of copies: 2 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-9S8:
Non-cubane [4Fe-4S]-cluster

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Macromolecule #10: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 10 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 203 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.6
Details: 50 mM Tris-HCl pH 7.6 containing 400 mM Ammonium sulfate.
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7768 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Details: Particles were C2-symmetry expanded / Number images used: 234858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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