[English] 日本語
Yorodumi
- EMDB-42773: structure of the K9me3-H2A.Z nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42773
Titlestructure of the K9me3-H2A.Z nucleosome
Map data
Sample
  • Complex: HP1alpha dimer bound to H2A.Z nucleosome
    • Protein or peptide: Histone H3, K9me3
    • Protein or peptide: Histone H2A.Z
    • Protein or peptide: Histone H2B
    • DNA: Widom601 (208bp) strand1
    • DNA: Widom601 (208bp) strand2
  • Protein or peptide: Histone H4
Keywordsheterochromatin / nucleosome / chromatin / GENE REGULATION / STRUCTURAL PROTEIN
Biological speciesEscherichia coli (E. coli) / Xenopus laevis (African clawed frog) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsTan D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133611 United States
CitationJournal: To Be Published
Title: Structure of human HP1 in complex with H2A.Z nucleosome
Authors: Tan D / Sokolova V
History
DepositionNov 9, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42773.png

Downloads & links

-
Map

FileDownload / File: emd_42773.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-1.7176292 - 2.8336658
Average (Standard dev.)0.0062578423 (±0.089734316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : HP1alpha dimer bound to H2A.Z nucleosome

EntireName: HP1alpha dimer bound to H2A.Z nucleosome
Components
  • Complex: HP1alpha dimer bound to H2A.Z nucleosome
    • Protein or peptide: Histone H3, K9me3
    • Protein or peptide: Histone H2A.Z
    • Protein or peptide: Histone H2B
    • DNA: Widom601 (208bp) strand1
    • DNA: Widom601 (208bp) strand2
  • Protein or peptide: Histone H4

-
Supramolecule #1: HP1alpha dimer bound to H2A.Z nucleosome

SupramoleculeName: HP1alpha dimer bound to H2A.Z nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#6, #10-#11
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 288 MDa

-
Macromolecule #1: Histone H3, K9me3

MacromoleculeName: Histone H3, K9me3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARK(me3) STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE L LIRKLPFQ RLVREIAQDF KTDLRFQSSA VMALQEASEA YLVALFEDTN LAAIHAKRVT IM PKDIQLA RRIRGERA

-
Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRD AVTYTEHAKR KTVTAMDVVY ALKRQGRTLY GFGG

-
Macromolecule #3: Histone H2A.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGGKAGKDS GKAKTKAVSR SQRAGLQFPV GRIHRHLKSR TTSHGRVGAT AAVYSAAILE YLTAEVLEL AGNASKDLKV KRITPRHLQL AIRGDEELDS LIKATIAGGG VIPHIHKSLI G KKGQQKTV

-
Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVND VFERIAGEAS RLAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV T KYTSAK

-
Macromolecule #5: Widom601 (208bp) strand1

MacromoleculeName: Widom601 (208bp) strand1 / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString: ACTCCGGCAA GGTCGCTGTT CAATACATGC ACAGGATGTA TATATCTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGTTAA AACGCGGGGG ACAGCGCGTA CGTGCGTTTA AGCGGTGCTA GAGCTGTCTA CGACCAATTG AGCGGCCTCG GCACCGGGAT ...String:
ACTCCGGCAA GGTCGCTGTT CAATACATGC ACAGGATGTA TATATCTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGTTAA AACGCGGGGG ACAGCGCGTA CGTGCGTTTA AGCGGTGCTA GAGCTGTCTA CGACCAATTG AGCGGCCTCG GCACCGGGAT TCTCCAGGGC GGCCGCGTAT AGGGTCCATC ACATAAGT

-
Macromolecule #6: Widom601 (208bp) strand2

MacromoleculeName: Widom601 (208bp) strand2 / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString: ACTTATGTGA TGGACCCTAT ACGCGGCCGC CCTGGAGAAT CCCGGTGCCG AGGCCGCTCA ATTGGTCGTA GACAGCTCTA GCACCGCTTA AACGCACGTA CGCGCTGTCC CCCGCGTTTT AACCGCCAAG GGGATTACTC CCTAGTCTCC AGGCACGTGT CAGATATATA ...String:
ACTTATGTGA TGGACCCTAT ACGCGGCCGC CCTGGAGAAT CCCGGTGCCG AGGCCGCTCA ATTGGTCGTA GACAGCTCTA GCACCGCTTA AACGCACGTA CGCGCTGTCC CCCGCGTTTT AACCGCCAAG GGGATTACTC CCTAGTCTCC AGGCACGTGT CAGATATATA CATCCTGTGC ATGTATTGAA CAGCGACCTT GCCGGAGT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 39.2 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
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 opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: Alphafold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 454841
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 23000 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5973


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient

+
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