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- EMDB-75527: DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (c... -

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Basic information

Entry
Database: EMDB / ID: EMD-75527
TitleDNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite)
Map data
Sample
  • Complex: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-H
    • Protein or peptide: Histone H2B type 2-F
    • DNA: 601 I strand (non-damaged strand)
    • DNA: 601 J strand (damaged strand 1)
    • DNA: 601 K strand (damaged strand 2)
  • Protein or peptide: DNA ligase 3
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsNucleosome / DNA Ligase IIIa / DNA Repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Strand-asynchronous mitochondrial DNA replication / double-strand break repair via alternative nonhomologous end joining / lagging strand elongation / HDR through MMEJ (alt-NHEJ) / Resolution of AP sites via the single-nucleotide replacement pathway ...DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Strand-asynchronous mitochondrial DNA replication / double-strand break repair via alternative nonhomologous end joining / lagging strand elongation / HDR through MMEJ (alt-NHEJ) / Resolution of AP sites via the single-nucleotide replacement pathway / mitochondrial DNA repair / DNA biosynthetic process / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / base-excision repair, gap-filling / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Gap-filling DNA repair synthesis and ligation in GG-NER / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / mitochondrion organization / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / base-excision repair / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / double-strand break repair via homologous recombination / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Metalloprotease DUBs / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / Gap-filling DNA repair synthesis and ligation in TC-NER / structural constituent of chromatin / UCH proteinases / nucleosome / double-strand break repair / heterochromatin formation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / gene expression / chromosome, telomeric region / Ub-specific processing proteases / mitochondrial matrix / Amyloid fiber formation / protein heterodimerization activity / cell division / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region
Similarity search - Function
DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal ...DNA ligase 3, BRCT domain / DNA ligase 3 BRCT domain / : / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / DNA ligase, ATP-dependent, conserved site / Zinc finger, PARP-type / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / : / 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 / 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 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA ligase 3 / Histone H4 / Histone H2B type 2-F / Histone H3.2 / Histone H2A type 1-H
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBoesch DJ / Weaver TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2
Authors: Boesch DJ / Weaver TM
History
DepositionFeb 12, 2026-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75527.png

Downloads & links

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Map

FileDownload / File: emd_75527.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.65 Å/pix.
x 400 pix.
= 260.8 Å		0.65 Å/pix.
x 400 pix.
= 260.8 Å		0.65 Å/pix.
x 400 pix.
= 260.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.5
Minimum - Maximum-14.297381 - 33.351306999999998
Average (Standard dev.)0.0034274906 (±1.0198855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 260.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2

EntireName: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2
Components
  • Complex: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-H
    • Protein or peptide: Histone H2B type 2-F
    • DNA: 601 I strand (non-damaged strand)
    • DNA: 601 J strand (damaged strand 1)
    • DNA: 601 K strand (damaged strand 2)
  • Protein or peptide: DNA ligase 3
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2

SupramoleculeName: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.228073 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSS AVMALQEASE AYLVGLFEDT NLAAIHAKRV TIMPKDIQL ARRIRGE

UniProtKB: Histone H3.2

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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: Homo sapiens (human)
Molecular weightTheoretical: 9.123692 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LRDNIQGITK PAIRRLARRG GVKRISGLIY EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGFG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-H

MacromoleculeName: Histone H2A type 1-H / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.692677 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRND EELNKLLGK VTIAQGGVLP NIQAVLLP

UniProtKB: Histone H2A type 1-H

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Macromolecule #4: Histone H2B type 2-F

MacromoleculeName: Histone H2B type 2-F / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.249723 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RKESYSVYVY KVLKQVHPDT GISSKAMGIM NSFVNDIFER IAGEASRLAH YNKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKY TSS

UniProtKB: Histone H2B type 2-F

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Macromolecule #8: DNA ligase 3

MacromoleculeName: DNA ligase 3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA ligase (ATP)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.847949 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QASLMTPVQP MLAEACKSVE YAMKKCPNGM FSEIKYDGER VQVHKNGDHF SYFSRSLKPV LPHKVAHFKD YIPQAFPGGH SMILDSEVL LIDNKTGKPL PFGTLGVHKK AAFQDANVCL FVFDCIYFND VSLMDRPLCE RRKFLHDNMV EIPNRIMFSE M KRVTKALD ...String:
QASLMTPVQP MLAEACKSVE YAMKKCPNGM FSEIKYDGER VQVHKNGDHF SYFSRSLKPV LPHKVAHFKD YIPQAFPGGH SMILDSEVL LIDNKTGKPL PFGTLGVHKK AAFQDANVCL FVFDCIYFND VSLMDRPLCE RRKFLHDNMV EIPNRIMFSE M KRVTKALD LADMITRVIQ EGLEGLVLKD VKGTYEPGKR HWLKVKKDYL

UniProtKB: DNA ligase 3

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Macromolecule #5: 601 I strand (non-damaged strand)

MacromoleculeName: 601 I strand (non-damaged strand) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.13877 KDa
SequenceString: (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(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)(DG)(DA)(DT)

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Macromolecule #6: 601 J strand (damaged strand 1)

MacromoleculeName: 601 J strand (damaged strand 1) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.352105 KDa
SequenceString: (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(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)

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Macromolecule #7: 601 K strand (damaged strand 2)

MacromoleculeName: 601 K strand (damaged strand 2) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 28.212986 KDa
SequenceString: (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) ...String:
(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)(DG)(DA)(DT)

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Macromolecule #9: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9dwf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #2

Image processing ID2
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9dwf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #3

Image processing ID3
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9dwf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #4

Image processing ID4
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9dwf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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