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- EMDB-42094: Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome ... -

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Basic information

Entry
Database: EMDB / ID: EMD-42094
TitleCryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map)
Map data
Sample
  • Complex: 162bp NRCAM nucleosome in complex with Asc1/E12a
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: NRCAM DNA (162-MER)
    • DNA: NRCAM DNA (162-MER)
    • Protein or peptide: scFv
    • Protein or peptide: Achaete-scute homolog 1
    • Protein or peptide: Transcription factor E2-alpha
Keywordsnucleosome / pioneer transcription factors / DNA binding proteins / transcription / NUCLEAR PROTEIN
Function / homology
Function and homology information


noradrenergic neuron fate commitment / spinal cord oligodendrocyte cell differentiation / spinal cord oligodendrocyte cell fate specification / oligodendrocyte cell fate commitment / regulation of timing of subpallium neuron differentiation / lung neuroendocrine cell differentiation / carotid body glomus cell differentiation / cerebral cortex GABAergic interneuron differentiation / subpallium neuron fate commitment / stomach neuroendocrine cell differentiation ...noradrenergic neuron fate commitment / spinal cord oligodendrocyte cell differentiation / spinal cord oligodendrocyte cell fate specification / oligodendrocyte cell fate commitment / regulation of timing of subpallium neuron differentiation / lung neuroendocrine cell differentiation / carotid body glomus cell differentiation / cerebral cortex GABAergic interneuron differentiation / subpallium neuron fate commitment / stomach neuroendocrine cell differentiation / ventral spinal cord interneuron fate commitment / commitment of neuronal cell to specific neuron type in forebrain / adrenal chromaffin cell differentiation / cellular response to magnetism / parasympathetic nervous system development / vestibular nucleus development / noradrenergic neuron development / musculoskeletal movement, spinal reflex action / olfactory pit development / GABAergic neuron differentiation / spinal cord association neuron differentiation / peripheral nervous system neuron development / neuroblast fate determination / neuroendocrine cell differentiation / regulation of epithelial cell differentiation / bHLH transcription factor binding / neuron fate specification / cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / natural killer cell differentiation / motor neuron migration / sympathetic ganglion development / lymphocyte differentiation / regulation of Notch signaling pathway / enteric nervous system development / neuron fate commitment / immunoglobulin V(D)J recombination / sympathetic nervous system development / Peyer's patch development / response to folic acid / Myogenesis / pattern specification process / response to epidermal growth factor / positive regulation of neural precursor cell proliferation / oligodendrocyte development / neural precursor cell proliferation / positive regulation of neurogenesis / generation of neurons / negative regulation of neuron differentiation / B cell lineage commitment / positive regulation of Notch signaling pathway / central nervous system neuron development / E-box binding / oligodendrocyte differentiation / regulation of G1/S transition of mitotic cell cycle / neuroblast proliferation / regulation of neurogenesis / response to retinoic acid / negative regulation of tumor necrosis factor-mediated signaling pathway / neuron development / : / cis-regulatory region sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / cell maturation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / Notch signaling pathway / CENP-A containing nucleosome / positive regulation of B cell proliferation / positive regulation of cell cycle / Packaging Of Telomere Ends / gastrulation / positive regulation of neuron differentiation / 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 / regulation of mitotic cell cycle / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / erythrocyte differentiation / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / innate immune response in mucosa / Defective pyroptosis
Similarity search - Function
Achaete-scute transcription factor-related / : / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / : / Histone H2B signature. / Histone H2A conserved site ...Achaete-scute transcription factor-related / : / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A 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
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Transcription factor E2-alpha / Histone H4 / Histone H3.1 / Achaete-scute homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhou BR / Bai Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Cryo-EM structure of NRCAM nucleosome aided by scFv
Authors: Zhou BR / Bai Y
History
DepositionSep 23, 2023-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42094.png

Downloads & links

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Map

FileDownload / File: emd_42094.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 337.92 Å		1.06 Å/pix.
x 320 pix.
= 337.92 Å		1.06 Å/pix.
x 320 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.018620921 - 0.048528265
Average (Standard dev.)0.000049947677 (±0.0010159509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42094_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42094_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 : 162bp NRCAM nucleosome in complex with Asc1/E12a

EntireName: 162bp NRCAM nucleosome in complex with Asc1/E12a
Components
  • Complex: 162bp NRCAM nucleosome in complex with Asc1/E12a
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: NRCAM DNA (162-MER)
    • DNA: NRCAM DNA (162-MER)
    • Protein or peptide: scFv
    • Protein or peptide: Achaete-scute homolog 1
    • Protein or peptide: Transcription factor E2-alpha

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Supramolecule #1: 162bp NRCAM nucleosome in complex with Asc1/E12a

SupramoleculeName: 162bp NRCAM nucleosome in complex with Asc1/E12a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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

UniProtKB: Histone H3.1

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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: 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-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.935239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: scFv

MacromoleculeName: scFv / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.34542 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV ...String:
MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV KMPCKASGYT FTSYTIQWVK QTPRQGLEWI GYIYPYNAGT KYNEKFKGKA TLTSDKSSST VYMELSSLTS ED SAVYYCA RKSSRLRSTL DYWGQGTSVT VSS

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Macromolecule #8: Achaete-scute homolog 1

MacromoleculeName: Achaete-scute homolog 1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.765484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MESSGKMESG AGQQPQPPQP FLPPAACFFA TAAAAAAAAA AAAQSAQQQQ PQAPPQQAPQ LSPVADSQPS GGGHKSAAKQ VKRQRSSSP ELMRCKRRLN FSGFGYSLPQ QQPAAVARRN ERERNRVKLV NLGFATLREH VPNGAANKKM SKVETLRSAV E YIRALQQL ...String:
MESSGKMESG AGQQPQPPQP FLPPAACFFA TAAAAAAAAA AAAQSAQQQQ PQAPPQQAPQ LSPVADSQPS GGGHKSAAKQ VKRQRSSSP ELMRCKRRLN FSGFGYSLPQ QQPAAVARRN ERERNRVKLV NLGFATLREH VPNGAANKKM SKVETLRSAV E YIRALQQL LDEHDAVSAA FQAGVLSPTI SPNYSNDLNS MAGSPVSSYS SDEGSYDPLS PEEQELLDFT NWF

UniProtKB: Achaete-scute homolog 1

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Macromolecule #9: Transcription factor E2-alpha

MacromoleculeName: Transcription factor E2-alpha / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 67.777461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMNQSQRMAP VGSDKELSDL LDFSMMFPLP VANGKSRPAS LGGTQFAGSG LEDRPSSGSW GSSDQNSSSF DPSRTYSEGA HFSDSHSSL PPSTFLGAGL GGKGSERNAY ATFGRDTSVG TLSQAGFLPG ELSLSSPGPL SPSGIKSSSQ YYPSFPSNPR R RAADGGLD ...String:
MMNQSQRMAP VGSDKELSDL LDFSMMFPLP VANGKSRPAS LGGTQFAGSG LEDRPSSGSW GSSDQNSSSF DPSRTYSEGA HFSDSHSSL PPSTFLGAGL GGKGSERNAY ATFGRDTSVG TLSQAGFLPG ELSLSSPGPL SPSGIKSSSQ YYPSFPSNPR R RAADGGLD TQPKKVRKVP PGLPSSVYPP SSGDSYSRDA AAYPSAKTPS SAYPSPFYVA DGSLHPSAEL WSTPSQVGFG PM LGDGSSP LPLAPGSSSV GSGTFGGLQQ QDRMGYQLHG SEVNGSLPAV SSFSAAPGTY SGTSGHTPPV SGAAAESLLG TRG TTASSS GDALGKALAS IYSPDHSSNN FSPSPSTPVG SPQGLPGTSQ WPRAGAPSAL SPNYDAGLHG LSKMEDRLDE AIHV LRSHA VGTASDLHGL LPGHGALTTS FTGPMSLGGR HAGLVGGSHP EEGLTSGASL LHNHASLPSQ PSSLPDLSQR PPDSY SGLG RAGTTAGASE IKREEKEDEE IASVADAEED KKDLKVPRTR TSPDEDEDDL LPPEQKAERE KERRVANNAR ERLRVR DIN EAFKELGRMC QLHLSSEKPQ TKLLILHQAV AVILSLEQQV RERNLNPKAA CLKRREEEKV SGVVGDPQLA LSAAHPG LG EAHNPAGHL

UniProtKB: Transcription factor E2-alpha

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Macromolecule #5: NRCAM DNA (162-MER)

MacromoleculeName: NRCAM DNA (162-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 49.86582 KDa
SequenceString: (DG)(DA)(DT)(DC)(DC)(DA)(DT)(DT)(DA)(DC) (DT)(DT)(DC)(DT)(DG)(DA)(DA)(DA)(DC)(DA) (DG)(DA)(DT)(DG)(DA)(DC)(DT)(DC)(DC) (DC)(DA)(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DC) (DT) (DG)(DC)(DC)(DT)(DG)(DT) ...String:
(DG)(DA)(DT)(DC)(DC)(DA)(DT)(DT)(DA)(DC) (DT)(DT)(DC)(DT)(DG)(DA)(DA)(DA)(DC)(DA) (DG)(DA)(DT)(DG)(DA)(DC)(DT)(DC)(DC) (DC)(DA)(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DC) (DT) (DG)(DC)(DC)(DT)(DG)(DT)(DG)(DG) (DC)(DC)(DC)(DA)(DC)(DA)(DG)(DG)(DG)(DC) (DT)(DT) (DC)(DC)(DT)(DG)(DC)(DC)(DC) (DT)(DG)(DC)(DA)(DT)(DG)(DA)(DC)(DA)(DG) (DC)(DT)(DG) (DC)(DA)(DC)(DA)(DT)(DC) (DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG) (DG)(DT)(DC)(DA) (DT)(DA)(DC)(DT)(DA) (DC)(DT)(DT)(DC)(DA)(DG)(DC)(DC)(DG)(DC) (DT)(DT)(DC)(DT)(DA) (DC)(DG)(DG)(DC) (DC)(DA)(DG)(DA)(DT)(DA)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DG)(DG) (DT)(DG)(DG) (DG)(DG)(DA)(DA)(DC)(DA)(DT)(DA)(DG)(DG) (DC)(DA)(DA)(DG)(DG)(DG)(DA) (DT)(DC)

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Macromolecule #6: NRCAM DNA (162-MER)

MacromoleculeName: NRCAM DNA (162-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 50.149953 KDa
SequenceString: (DG)(DA)(DT)(DC)(DC)(DC)(DT)(DT)(DG)(DC) (DC)(DT)(DA)(DT)(DG)(DT)(DT)(DC)(DC)(DC) (DC)(DA)(DC)(DC)(DC)(DA)(DC)(DT)(DT) (DT)(DT)(DG)(DT)(DA)(DT)(DC)(DT)(DG)(DG) (DC) (DC)(DG)(DT)(DA)(DG)(DA) ...String:
(DG)(DA)(DT)(DC)(DC)(DC)(DT)(DT)(DG)(DC) (DC)(DT)(DA)(DT)(DG)(DT)(DT)(DC)(DC)(DC) (DC)(DA)(DC)(DC)(DC)(DA)(DC)(DT)(DT) (DT)(DT)(DG)(DT)(DA)(DT)(DC)(DT)(DG)(DG) (DC) (DC)(DG)(DT)(DA)(DG)(DA)(DA)(DG) (DC)(DG)(DG)(DC)(DT)(DG)(DA)(DA)(DG)(DT) (DA)(DG) (DT)(DA)(DT)(DG)(DA)(DC)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DG) (DA)(DT)(DG) (DT)(DG)(DC)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DA)(DT)(DG)(DC)(DA)(DG) (DG)(DG)(DC)(DA) (DG)(DG)(DA)(DA)(DG) (DC)(DC)(DC)(DT)(DG)(DT)(DG)(DG)(DG)(DC) (DC)(DA)(DC)(DA)(DG) (DG)(DC)(DA)(DG) (DC)(DA)(DG)(DC)(DT)(DG)(DC)(DT)(DG)(DG) (DG)(DA)(DG)(DT)(DC)(DA) (DT)(DC)(DT) (DG)(DT)(DT)(DT)(DC)(DA)(DG)(DA)(DA)(DG) (DT)(DA)(DA)(DT)(DG)(DG)(DA) (DT)(DC)

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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: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 237174
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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