[English] 日本語
Yorodumi
- EMDB-32148: NuA4 HAT module bound to the nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32148
TitleNuA4 HAT module bound to the nucleosome
Map data
Sample
  • Complex: complex of NuA4 HAT module and nucleosome
    • Protein or peptide: x 8 types
    • DNA: x 2 types
  • Ligand: x 1 types
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / : / piccolo histone acetyltransferase complex / SUMOylation of transcription cofactors / NuA4 histone acetyltransferase complex / positive regulation of macroautophagy / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / methylated histone binding ...PI5P Regulates TP53 Acetylation / : / piccolo histone acetyltransferase complex / SUMOylation of transcription cofactors / NuA4 histone acetyltransferase complex / positive regulation of macroautophagy / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / methylated histone binding / meiotic cell cycle / structural constituent of chromatin / nucleosome / chromatin organization / cell cycle / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / Enhancer of polycomb protein / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type ...Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / Enhancer of polycomb protein / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / Zinc finger, PHD-type, conserved site / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / 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 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone H3 / Chromatin modification-related protein EAF6 / Histone acetyltransferase ESA1 / Histone H2B 1.1 / Chromatin modification-related protein YNG2 / Enhancer of polycomb-like protein 1 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen Z / Qu K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structure of the NuA4 acetyltransferase complex bound to the nucleosome.
Authors: Keke Qu / Kangjing Chen / Hao Wang / Xueming Li / Zhucheng Chen /
Abstract: Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an ...Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an important role in the formation of high-order chromatin structure and heterochromatin silencing. NuA4 in yeast and its homologue Tip60 complex in mammalian cells are the key enzymes that catalyse H4 acetylation, which in turn regulates chromatin packaging and function in transcription activation and DNA repair. Here we report the cryo-electron microscopy structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome. NuA4 comprises two major modules: the catalytic histone acetyltransferase (HAT) module and the transcription activator-binding (TRA) module. The nucleosome is mainly bound by the HAT module and is positioned close to a polybasic surface of the TRA module, which is important for the optimal activity of NuA4. The nucleosomal linker DNA carrying the upstream activation sequence is oriented towards the conserved, transcription activator-binding surface of the Tra1 subunit, which suggests a potential mechanism of NuA4 to act as a transcription co-activator. The HAT module recognizes the disk face of the nucleosome through the H2A-H2B acidic patch and nucleosomal DNA, projecting the catalytic pocket of Esa1 to the N-terminal tail of H4 and supporting its function in selective acetylation of H4. Together, our findings illustrate how NuA4 is assembled and provide mechanistic insights into nucleosome recognition and transcription co-activation by a HAT.
History
DepositionNov 9, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32148.png

Downloads & links

-
Map

FileDownload / File: emd_32148.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.014078226 - 0.045995325
Average (Standard dev.)8.745577e-05 (±0.0010561035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 407.02 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : complex of NuA4 HAT module and nucleosome

EntireName: complex of NuA4 HAT module and nucleosome
Components
  • Complex: complex of NuA4 HAT module and nucleosome
    • Protein or peptide: Chromatin modification-related protein EAF6
    • Protein or peptide: Chromatin modification-related protein YNG2
    • Protein or peptide: Enhancer of polycomb-like protein 1
    • Protein or peptide: Histone H3
    • Protein or peptide: H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone acetyltransferase ESA1
    • DNA: DNA (207-mer)
    • DNA: DNA (207-mer)
  • Ligand: CARBOXYMETHYL COENZYME *A

+
Supramolecule #1: complex of NuA4 HAT module and nucleosome

SupramoleculeName: complex of NuA4 HAT module and nucleosome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: Chromatin modification-related protein EAF6

MacromoleculeName: Chromatin modification-related protein EAF6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 12.915704 KDa
SequenceString:
MTDELKSYEA LKAELKKSLQ DRREQEDTFD NLQQEIYDKE TEYFSHNSNN NHSGHGGAHG SKSHYSGNII KGFDTFSKSH HSHADSAFN NNDRIFSLSS ATYVKQQHGQ SQND

+
Macromolecule #2: Chromatin modification-related protein YNG2

MacromoleculeName: Chromatin modification-related protein YNG2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 32.139514 KDa
SequenceString: MDPSLVLEQT IQDVSNLPSE FRYLLEEIGS NDLKLIEEKK KYEQKESQIH KFIRQQGSIP KHPQEDGLDK EIKESLLKCQ SLQREKCVL ANTALFLIAR HLNKLEKNIA LLEEDGVLAP VEEDGDMDSA AEASRESSVV SNSSVKKRRA ASSSGSVPPT L KKKKTSRT ...String:
MDPSLVLEQT IQDVSNLPSE FRYLLEEIGS NDLKLIEEKK KYEQKESQIH KFIRQQGSIP KHPQEDGLDK EIKESLLKCQ SLQREKCVL ANTALFLIAR HLNKLEKNIA LLEEDGVLAP VEEDGDMDSA AEASRESSVV SNSSVKKRRA ASSSGSVPPT L KKKKTSRT SKLQNEIDVS SREKSVTPVS PSIEKKIART KEFKNSRNGK GQNGSPENEE EDKTLYCFCQ RVSFGEMVAC DG PNCKYEW FHYDCVNLKE PPKGTWYCPE CKIEMEKNKL KRKRN

+
Macromolecule #3: Enhancer of polycomb-like protein 1

MacromoleculeName: Enhancer of polycomb-like protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 96.889867 KDa
SequenceString: MPTPSNAIEI NDGSHKSGRS TRRSGSRSAH DDGLDSFSKG DSGAGASAGS SNSRFRHRKI SVKQHLKIYL PNDLKHLDKD ELQQREVVE IETGVEKNEE KEVHLHRILQ MGSGHTKHKD YIPTPDASMT WNEYDKFYTG SFQETTSYIK FSATVEDCCG T NYNMDERD ...String:
MPTPSNAIEI NDGSHKSGRS TRRSGSRSAH DDGLDSFSKG DSGAGASAGS SNSRFRHRKI SVKQHLKIYL PNDLKHLDKD ELQQREVVE IETGVEKNEE KEVHLHRILQ MGSGHTKHKD YIPTPDASMT WNEYDKFYTG SFQETTSYIK FSATVEDCCG T NYNMDERD ETFLNEQVNK GSSDILTEDE FEILCSSFEH AIHERQPFLS MDPESILSFE ELKPTLIKSD MADFNLRNQL NH EINSHKT HFITQFDPVS QMNTRPLIQL IEKFGSKIYD YWRERKIEVN GYEIFPQLKF ERPGEKEEID PYVCFRRREV RHP RKTRRI DILNSQRLRA LHQELKNAKD LALLVAKREN VSLNWINDEL KIFDQRVKIK NLKRSLNISG EDDDLINHKR KRPT IVTVE QREAELRKAE LKRAAAAAAA AKAKNNKRNN QLEDKSSRLT KQQQQQLLQQ QQQQQQNALK TENGKQLANA SSSST SQPI TSHVYVKLPS SKIPDIVLED VDALLNSKEK NARKFVQEKM EKRKIEDADV FFNLTDDPFN PVFDMSLPKN FSTSNV PFA SIASSKFQID RSFYSSHLPE YLKGISDDIR IYDSNGRSRN KDNYNLDTKR IKKTELYDPF QENLEIHSRE YPIKFRK RV GRSNIKYVDR MPNFTTSSTK SACSLMDFVD FDSIEKEQYS REGSNDTDSI NVYDSKYDEF VRLYDKWKYD SPQNEYGI K FSDEPARLNQ ISNDTQVIRF GTMLGTKSYE QLREATIKYR RDYITRLKQK HIQHLQQQQQ QQQQQQQQAQ QQKQKSQNN NSNSSNSLKK LNDSLINSEA KQNSSITQKN SS

+
Macromolecule #4: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

+
Macromolecule #5: H4

MacromoleculeName: H4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

+
Macromolecule #6: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

+
Macromolecule #7: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

+
Macromolecule #8: Histone acetyltransferase ESA1

MacromoleculeName: Histone acetyltransferase ESA1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 52.692844 KDa
SequenceString: MSHDGKEEPG IAKKINSVDD IIIKCQCWVQ KNDEERLAEI LSINTRKAPP KFYVHYVNYN KRLDEWITTD RINLDKEVLY PKLKATDED NKKQKKKKAT NTSETPQDSL QDGVDGFSRE NTDVMDLDNL NVQGIKDENI SHEDEIKKLR TSGSMTQNPH E VARVRNLN ...String:
MSHDGKEEPG IAKKINSVDD IIIKCQCWVQ KNDEERLAEI LSINTRKAPP KFYVHYVNYN KRLDEWITTD RINLDKEVLY PKLKATDED NKKQKKKKAT NTSETPQDSL QDGVDGFSRE NTDVMDLDNL NVQGIKDENI SHEDEIKKLR TSGSMTQNPH E VARVRNLN RIIMGKYEIE PWYFSPYPIE LTDEDFIYID DFTLQYFGSK KQYERYRKKC TLRHPPGNEI YRDDYVSFFE ID GRKQRTW CRNLCLLSKL FLDHKTLYYD VDPFLFYCMT RRDELGHHLV GYFSKEKESA DGYNVACILT LPQYQRMGYG KLL IEFSYE LSKKENKVGS PEKPLSDLGL LSYRAYWSDT LITLLVEHQK EITIDEISSM TSMTTTDILH TAKTLNILRY YKGQ HIIFL NEDILDRYNR LKAKKRRTID PNRLIWKPPV FTASQLRFAW

+
Macromolecule #9: DNA (207-mer)

MacromoleculeName: DNA (207-mer) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 63.679512 KDa
SequenceString: (DT)(DC)(DC)(DG)(DG)(DA)(DG)(DG)(DA)(DC) (DT)(DG)(DT)(DC)(DC)(DT)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC) (DC) (DA)(DT)(DC)(DG)(DA)(DG) ...String:
(DT)(DC)(DC)(DG)(DG)(DA)(DG)(DG)(DA)(DC) (DT)(DG)(DT)(DC)(DC)(DT)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC) (DC) (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)(DA)(DG)(DC)(DT) (DT)(DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DG)(DT)(DA)(DC)(DT)(DA)(DG)

+
Macromolecule #10: DNA (207-mer)

MacromoleculeName: DNA (207-mer) / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 64.150809 KDa
SequenceString: (DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (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) ...String:
(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (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)(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)(DG)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT) (DA) (DG)(DG)(DG)(DT)(DC)(DC)(DC)(DC)(DG)(DG) (DA)(DG)(DG)(DA)(DC)(DA)(DG)(DT)(DC) (DC)(DT)(DC)(DC)(DG)(DG)(DA)

+
Macromolecule #11: CARBOXYMETHYL COENZYME *A

MacromoleculeName: CARBOXYMETHYL COENZYME *A / type: ligand / ID: 11 / Number of copies: 1 / Formula: CMC
Molecular weightTheoretical: 825.57 Da
Chemical component information

ChemComp-CMC:
CARBOXYMETHYL COENZYME *A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TITAN 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: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 393016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more