[English] 日本語
Yorodumi
- EMDB-17797: human RYBP-PRC1 bound to mononucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17797
Titlehuman RYBP-PRC1 bound to mononucleosome
Map dataSharpened map
Sample
  • Complex: human RYBP-PRC1 bound to nucleosome
    • Complex: RING1B:BMI1 heterodimer
      • Protein or peptide: Polycomb complex protein BMI-1
      • Protein or peptide: E3 ubiquitin-protein ligase RING2
    • Complex: Drosophila octamer
      • Protein or peptide: Histone H3 (Fragment)
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA (215-mer)
      • DNA: DNA (215-mer)
  • Ligand: ZINC ION
KeywordsncPRC1 complex / nucleosome / H2A / histones / RING1B / BMI1 / heterodimer / E3 ligase / K119 / GENE REGULATION
Function / homology
Function and homology information


regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression ...regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / RING-like zinc finger domain binding / Oxidative Stress Induced Senescence / PRC1 complex / sex chromatin / rostrocaudal neural tube patterning / segment specification / polytene chromosome / ubiquitin-protein transferase activator activity / embryonic skeletal system morphogenesis / somatic stem cell division / PcG protein complex / positive regulation of immature T cell proliferation in thymus / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / negative regulation of gene expression, epigenetic / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / MLL1 complex / hemopoiesis / humoral immune response / negative regulation of apoptotic signaling pathway / heterochromatin / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / positive regulation of B cell proliferation / nucleosomal DNA binding / epigenetic regulation of gene expression / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / apoptotic signaling pathway / Regulation of PTEN gene transcription / promoter-specific chromatin binding / brain development / RING-type E3 ubiquitin transferase / euchromatin / negative regulation of DNA-binding transcription factor activity / heterochromatin formation / structural constituent of chromatin / positive regulation of fibroblast proliferation / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / chromatin organization / mitotic cell cycle / chromosome / gene expression / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / nuclear body / protein ubiquitination / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Histone H2B signature. / Histone H2B ...E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / 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. / Zinc finger RING-type profile. / Histone H3 signature 2. / Zinc finger, RING-type / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H4 / Histone H3 / Histone H2B / Polycomb complex protein BMI-1 / Histone H2A / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human) / Drosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsCiapponi M / Benda C / Mueller J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1.
Authors: Maria Ciapponi / Elena Karlukova / Sven Schkölziger / Christian Benda / Jürg Müller /
Abstract: Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified ...Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes.
History
DepositionJul 6, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17797.png

Downloads & links

-
Map

FileDownload / File: emd_17797.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0283144 - 2.01102
Average (Standard dev.)0.00297312 (±0.06992465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A

Fileemd_17797_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_17797_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : human RYBP-PRC1 bound to nucleosome

EntireName: human RYBP-PRC1 bound to nucleosome
Components
  • Complex: human RYBP-PRC1 bound to nucleosome
    • Complex: RING1B:BMI1 heterodimer
      • Protein or peptide: Polycomb complex protein BMI-1
      • Protein or peptide: E3 ubiquitin-protein ligase RING2
    • Complex: Drosophila octamer
      • Protein or peptide: Histone H3 (Fragment)
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA (215-mer)
      • DNA: DNA (215-mer)
  • Ligand: ZINC ION

+
Supramolecule #1: human RYBP-PRC1 bound to nucleosome

SupramoleculeName: human RYBP-PRC1 bound to nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #2: RING1B:BMI1 heterodimer

SupramoleculeName: RING1B:BMI1 heterodimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: Drosophila octamer

SupramoleculeName: Drosophila octamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Drosophila melanogaster (fruit fly)

+
Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Polycomb complex protein BMI-1

MacromoleculeName: Polycomb complex protein BMI-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.152359 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHRTTRIKIT ELNPHLMCVL CGGYFIDATT IIECLHSFCK TCIVRYLETS KYCPICDVQV HKTRPLLNIR SDKTLQDIVY KLVPGLFKN EMKRRRDFYA AHPSADAANG SNEDRGEVAD EDKRIITDDE IISLSIEFFD QNRLDRKVNK DKEKSKEEVN D KRYLRCPA ...String:
MHRTTRIKIT ELNPHLMCVL CGGYFIDATT IIECLHSFCK TCIVRYLETS KYCPICDVQV HKTRPLLNIR SDKTLQDIVY KLVPGLFKN EMKRRRDFYA AHPSADAANG SNEDRGEVAD EDKRIITDDE IISLSIEFFD QNRLDRKVNK DKEKSKEEVN D KRYLRCPA AMTVMHLRKF LRSKMDIPNT FQIDVMYEEE PLKDYYTLMD IAYIYTWRRN GPLPLKYRVR PTCKRMKISH QR DGLTNAG ELESDSGSDK ANSPAGGIPS TSSCLPSPST PVQSPHPQFP HISSTMNGTS NSPSGNHQSS FANRPRKSSV NGS SATSSG GMKHHHHHH

UniProtKB: Polycomb complex protein BMI-1

+
Macromolecule #2: E3 ubiquitin-protein ligase RING2

MacromoleculeName: E3 ubiquitin-protein ligase RING2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.062707 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPDSMSQAVQ TNGTQPLSKT WELSLYELQR TPQEAITDGL EIVVSPRSLH SELMCPICLD MLKNTMTTKE CLHRFCADCI ITALRSGNK ECPTCRKKLV SKRSLRPDPN FDALISKIYP SRDEYEAHQE RVLARINKHN NQQALSHSIE EGLKIQAMNR L QRGKKQQI ...String:
GPDSMSQAVQ TNGTQPLSKT WELSLYELQR TPQEAITDGL EIVVSPRSLH SELMCPICLD MLKNTMTTKE CLHRFCADCI ITALRSGNK ECPTCRKKLV SKRSLRPDPN FDALISKIYP SRDEYEAHQE RVLARINKHN NQQALSHSIE EGLKIQAMNR L QRGKKQQI ENGSGAEDNG DSSHCSNAST HSNQEAGPSN KRTKTSDDSG LELDNNNAAM AIDPVMDGAS EIELVFRPHP TL MEKDDSA QTRYIKTSGN ATVDHLSKYL AVRLALEELR SKGESNQMNL DTASEKQYTI YIATASGQFT VLNGSFSLEL VSE KYWKVN KPMELYYAPT KEHK

UniProtKB: E3 ubiquitin-protein ligase RING2

+
Macromolecule #3: Histone H3 (Fragment)

MacromoleculeName: Histone H3 (Fragment) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 15.289904 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

+
Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 11.521611 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MITGRGKGGK GLGKGGAKRH RKVLRDNIQG ITKPAIRRLA RRGGVKRISG LIYEETRGVL KVFLENVIRD AVTYTEHAKR KTVTAMDVV YALKRQGRTL YGFGG

UniProtKB: Histone H4

+
Macromolecule #5: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.257529 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKVK GKAKSRSNRA GLQFPVGRIH RLLRKGNYAE RVGAGAPVYL AAVMEYLAAE VLELAGNAAR DNKKTRIIPR HLQLAIRND EELNKLLSGV TIAQGGVLPN IQAVLLPKKT EKKA

UniProtKB: Histone H2A

+
Macromolecule #6: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.727064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPPKTSGKAA KKAGKAQKNI TKTDKKKKRK RKESYAIYIY KVLKQVHPDT GISSKAMSIM NSFVNDIFER IAAEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSSK

UniProtKB: Histone H2B

+
Macromolecule #7: DNA (215-mer)

MacromoleculeName: DNA (215-mer) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.716836 KDa
SequenceString: (DC)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG)(DC) (DA)(DT)(DG)(DC)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DC)(DG)(DA)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DA)(DT)(DA)(DT)(DC)(DC) (DC) (DG)(DA)(DG)(DT)(DC)(DG) ...String:
(DC)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG)(DC) (DA)(DT)(DG)(DC)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DC)(DG)(DA)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DA)(DT)(DA)(DT)(DC)(DC) (DC) (DG)(DA)(DG)(DT)(DC)(DG)(DC)(DT) (DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA)(DA)(DA) (DT)(DA) (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)(DT)(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)(DT) (DC)(DC)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DA) (DT)(DA)(DG)(DG)(DG)(DT)(DC)(DC)(DA) (DT)(DC)(DA)(DC)(DA)(DT)(DA)(DA)(DG)(DC) (DC) (DC)(DG)(DA)(DG)(DA)(DT)(DA)(DT)

+
Macromolecule #8: DNA (215-mer)

MacromoleculeName: DNA (215-mer) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.481609 KDa
SequenceString: (DA)(DT)(DA)(DT)(DC)(DT)(DC)(DG)(DG)(DG) (DC)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DG)(DG)(DA) (DC) (DC)(DT)(DG)(DG)(DA)(DG) ...String:
(DA)(DT)(DA)(DT)(DC)(DT)(DC)(DG)(DG)(DG) (DC)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DG)(DG)(DA) (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)(DT)(DA)(DT) (DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG)(DC)(DG)(DA)(DC)(DT)(DC)(DG)(DG) (DG)(DA)(DT)(DA)(DT)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DT)(DC)(DG)(DA)(DC)(DC) (DT)(DG)(DC)(DA)(DG)(DG)(DC)(DA)(DT)(DG) (DC) (DA)(DA)(DG)(DC)(DT)(DT)(DG)(DG)

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146136
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)

+
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://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