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- EMDB-72318: Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer b... -

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Basic information

Entry
Database: EMDB / ID: EMD-72318
TitleComposite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome
Map data
Sample
  • Complex: DNMT3A/3B tetramer bound to 167H3K36me2-nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (162-MER)
    • DNA: DNA (162-MER)
    • Protein or peptide: Isoform 7 of DNA (cytosine-5)-methyltransferase 3B
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
  • Ligand: ZINC ION
  • Ligand: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
KeywordsDNMT3A2-DNMT3B3 / DNA methylation / 167H3K36me2-nucleosome / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / transposable element silencing by piRNA-mediated DNA methylation / positive regulation of cellular response to hypoxia / protein-cysteine methyltransferase activity / DNA-methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / transposable element silencing by piRNA-mediated DNA methylation / positive regulation of cellular response to hypoxia / protein-cysteine methyltransferase activity / DNA-methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / SUMOylation of DNA methylation proteins / XY body / response to vitamin A / DNA methylation-dependent constitutive heterochromatin formation / hepatocyte apoptotic process / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / cellular response to ethanol / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / post-embryonic development / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / cellular response to amino acid stimulus / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / euchromatin / NoRC negatively regulates rRNA expression / response to lead ion / response to toxic substance / nuclear matrix / RMTs methylate histone arginines / neuron differentiation / structural constituent of chromatin / transcription corepressor activity / response to estradiol / heterochromatin formation / nucleosome / nucleosome assembly / spermatogenesis / methylation / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / DNA (cytosine-5)-methyltransferase 3B, ADD domain / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / DNA (cytosine-5)-methyltransferase 3B, ADD domain / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / : / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / DNA (cytosine-5)-methyltransferase 3B / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXie X / Zhou XE / Worden EJ / Jones PA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209859 United States
CitationJournal: To Be Published
Title: The structure basis for de novo DNA methylation in chromatin
Authors: Xie X / Liu M / Zhou XE / Worden EJ / Jones PA
History
DepositionAug 25, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72318.png

Downloads & links

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Map

FileDownload / File: emd_72318.map.gz / Format: CCP4 / Size: 57.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 251 pix.
= 415.656 Å		1.66 Å/pix.
x 244 pix.
= 404.064 Å		1.66 Å/pix.
x 247 pix.
= 409.032 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.004163648 - 9.962331000000001
Average (Standard dev.)0.008088293 (±0.12313947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-16-17-22
Dimensions244247251
Spacing247244251
CellA: 409.032 Å / B: 404.064 Å / C: 415.656 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DNMT3A/3B tetramer bound to 167H3K36me2-nucleosome

EntireName: DNMT3A/3B tetramer bound to 167H3K36me2-nucleosome
Components
  • Complex: DNMT3A/3B tetramer bound to 167H3K36me2-nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (162-MER)
    • DNA: DNA (162-MER)
    • Protein or peptide: Isoform 7 of DNA (cytosine-5)-methyltransferase 3B
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
  • Ligand: ZINC ION
  • Ligand: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine

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Supramolecule #1: DNMT3A/3B tetramer bound to 167H3K36me2-nucleosome

SupramoleculeName: DNMT3A/3B tetramer bound to 167H3K36me2-nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Details: Lys36 di-methylation / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.330975 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGV(MLY)KPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Details: Histone H2A / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Details: Histone H2B / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Isoform 7 of DNA (cytosine-5)-methyltransferase 3B

MacromoleculeName: Isoform 7 of DNA (cytosine-5)-methyltransferase 3B / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.568391 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: DSQQGGMESP QVEADSGDGD SSEYQDGKEF GIGDLVWGKI KGFSWWPAMV VSWKATSKRQ AMSGMRWVQW FGDGKFSEVS ADKLVALGL FSQHFNLATF NKLVSYRKAM YHALEKARVR AGKTFPSSPG DSLEDQLKPM LEWAHGGFKP TGIEGLKPNN T QPENKTRR ...String:
DSQQGGMESP QVEADSGDGD SSEYQDGKEF GIGDLVWGKI KGFSWWPAMV VSWKATSKRQ AMSGMRWVQW FGDGKFSEVS ADKLVALGL FSQHFNLATF NKLVSYRKAM YHALEKARVR AGKTFPSSPG DSLEDQLKPM LEWAHGGFKP TGIEGLKPNN T QPENKTRR RTADDSATSD YCPAPKRLKT NCYNNGKDRG DEKDYDQSRE QMASDVANNK SSLEDGCLSC GRKNPVSFHP LF EGGLCQT CRDRFLELFY MYDDDGYQSY CTVCCEGREL LLCSNTSCCR CFCVECLEVL VGTGTAAEAK LQEPWSCYMC LPQ RCHGVL RRRKDWNVRL QAFFTSDTGL EYEAPKLYPA IPAARRRPIR VLSLFDGIAT GYLVLKELGI KVGKYVASEV CEES IAVGT VKHEGNIKYV NDVRNITKKN IEEWGPFDLV IGGSPCNDLS NVNPARKGLY EGTGRLFFEF YHLLNYSRPK EGDDR PFFW MFENVVAMKV GDKRDISRFL ECNPVMIDAI KVSAAHRARY FWGNLPGMNR IFGFPVHYTD VSNMGRGARQ KLLGRS WSV PVIRHLFAPL KDYFACE

UniProtKB: DNA (cytosine-5)-methyltransferase 3B

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Macromolecule #8: DNA (cytosine-5)-methyltransferase 3A

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3A / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.914711 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MNAVEENQGP GESQKVEEAS PPAVQQPTDP ASPTVATTPE PVGSDAGDKN ATKAGDDEPE YEDGRGFGIG ELVWGKLRGF SWWPGRIVS WWMTGRSRAA EGTRWVMWFG DGKFSVVCVE KLMPLSSFCS AFHQATYNKQ PMYRKAIYEV LQVASSRAGK L FPVCHDSD ...String:
MNAVEENQGP GESQKVEEAS PPAVQQPTDP ASPTVATTPE PVGSDAGDKN ATKAGDDEPE YEDGRGFGIG ELVWGKLRGF SWWPGRIVS WWMTGRSRAA EGTRWVMWFG DGKFSVVCVE KLMPLSSFCS AFHQATYNKQ PMYRKAIYEV LQVASSRAGK L FPVCHDSD ESDTAKAVEV QNKPMIEWAL GGFQPSGPKG LEPPEEEKNP YKEVYTDMWV EPEAAAYAPP PPAKKPRKST AE KPKVKEI IDERTRERLV YEVRQKCRNI EDICISCGSL NVTLEHPLFV GGMCQNCKNC FLECAYQYDD DGYQSYCTIC CGG REVLMC GNNNCCRCFC VECVDLLVGP GAAQAAIKED PWNCYMCGHK GTYGLLRRRE DWPSRLQMFF ANNHDQEFDP PKVY PPVPA EKRKPIRVLS LFDGIATGLL VLKDLGIQVD RYIASEVCED SITVGMVRHQ GKIMYVGDVR SVTQKHIQEW GPFDL VIGG SPCNDLSIVN PARKGLYEGT GRLFFEFYRL LHDARPKEGD DRPFFWLFEN VVAMGVSDKR DISRFLESNP VMIDAK EVS AAHRARYFWG NLPGMNRPLA STVNDKLELQ ECLEHGRIAK FSKVRTITTR SNSIKQGKDQ HFPVFMNEKE DILWCTE ME RVFGFPVHYT DVSNMSRLAR QRLLGRSWSV PVIRHLFAPL KEYFACV

UniProtKB: DNA (cytosine-5)-methyltransferase 3A

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Macromolecule #5: DNA (162-MER)

MacromoleculeName: DNA (162-MER) / type: dna / ID: 5 / Details: 167bp DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.785953 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG) (DA)(DG)(DA)(DC)(DT)(DA) ...String:
(DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA) (DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DG)(DC) (DG)(DG) (DC)(DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (162-MER)

MacromoleculeName: DNA (162-MER) / type: dna / ID: 6 / Details: 167bp DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.327652 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA) (DT)(DT)(DG)(DG)(DT)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG) (DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC) (DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DG)(DC) (DG)(DG) (DC)(DC)(DG)(DA)(DT)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 9 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine

MacromoleculeName: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
type: ligand / ID: 10 / Number of copies: 2 / Formula: SAO
Molecular weightTheoretical: 385.419 Da
Chemical component information

ChemComp-SAO:
5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7152655
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6p7a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 652144
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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