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- EMDB-31816: Telomeric trinucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-31816
TitleTelomeric trinucleosome
Map data
Sample
  • Complex: Telomeric Mononucleosome
    • Protein or peptide: Histone H3.1Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • DNA: DNA (408-mer)
    • DNA: DNA (408-mer)
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / 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 ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site ...Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B type 1-K / Histone H2A type 1-B/E / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsSoman A
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Nature / Year: 2022
Title: Columnar structure of human telomeric chromatin.
Authors: Aghil Soman / Sook Yi Wong / Nikolay Korolev / Wahyu Surya / Simon Lattmann / Vinod K Vogirala / Qinming Chen / Nikolay V Berezhnoy / John van Noort / Daniela Rhodes / Lars Nordenskiöld /
Abstract: Telomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response. Little is known about the structure of telomeric ...Telomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response. Little is known about the structure of telomeric chromatin at the molecular level. Here we used negative stain electron microscopy and single-molecule magnetic tweezers to characterize 3-kbp-long telomeric chromatin fibres. We also obtained the cryogenic electron microscopy structure of the condensed telomeric tetranucleosome and its dinucleosome unit. The structure displayed close stacking of nucleosomes with a columnar arrangement, and an unusually short nucleosome repeat  length that comprised about 132 bp DNA wound in a continuous superhelix around histone octamers. This columnar structure is primarily stabilized by the H2A carboxy-terminal and histone amino-terminal tails in a synergistic manner. The columnar conformation results in exposure of the DNA helix, which may make it susceptible to both DNA damage and the DNA damage response. The conformation also exists in an alternative open state, in which one nucleosome is unstacked and flipped out, which exposes the acidic patch of the histone surface. The structural features revealed in this work suggest mechanisms by which protein factors involved in telomere maintenance can access telomeric chromatin in its compact form.
History
DepositionAug 25, 2021-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateOct 12, 2022-
Current statusOct 12, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31816.png

Downloads & links

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Map

FileDownload / File: emd_31816.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.0089
Minimum - Maximum-0.009205407 - 0.04153312
Average (Standard dev.)8.194096e-05 (±0.0028221342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 313.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_31816_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31816_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_31816_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Telomeric Mononucleosome

EntireName: Telomeric Mononucleosome
Components
  • Complex: Telomeric Mononucleosome
    • Protein or peptide: Histone H3.1Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • DNA: DNA (408-mer)
    • DNA: DNA (408-mer)

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Supramolecule #1: Telomeric Mononucleosome

SupramoleculeName: Telomeric Mononucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Mononucleosome in open statae in a telomeric tetranucleosome
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

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Macromolecule #4: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.151906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KKRKRSRKES YSVYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNKR STITSREIQT AVRLLLPGEL AKHAVSEGT KAVTKYTSAK

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Macromolecule #5: DNA (408-mer)

MacromoleculeName: DNA (408-mer) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.781156 KDa
SequenceString: (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG) (DG)(DG)(DT)(DT)(DA)(DG) ...String:
(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)

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Macromolecule #6: DNA (408-mer)

MacromoleculeName: DNA (408-mer) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.229008 KDa
SequenceString: (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT) (DA)(DA)(DC)(DC)(DC)(DT) ...String:
(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)

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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: 6
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %
Detailstri-NCP subunit of telomeric tetranucleosome

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 42654
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ke9

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7v9j:
Telomeric trinucleosome

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