[English] 日本語
Yorodumi
- EMDB-42774: Structure of Heterochromatin Protein 1 (HP1) alpha in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42774
TitleStructure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome
Map dataprimary map, consensus refinement with mask
Sample
  • Complex: HP1alpha dimer bound to H2A.Z nucleosome
    • Protein or peptide: Chromobox protein homolog 5
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.Z
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA Widom601 (208bp) strand1
    • DNA: DNA Widom601 (208bp) strand2
Keywordsheterochromatin / nucleosome / chromatin / GENE REGULATION / STRUCTURAL PROTEIN
Function / homology
Function and homology information


chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / pericentric heterochromatin / ribonucleoprotein complex binding / nucleosomal DNA binding ...chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / pericentric heterochromatin / ribonucleoprotein complex binding / nucleosomal DNA binding / transcription repressor complex / methylated histone binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of chromatin organization proteins / cellular response to estradiol stimulus / euchromatin / heterochromatin formation / kinetochore / histone deacetylase binding / cellular response to insulin stimulus / structural constituent of chromatin / nucleosome / nucleosome assembly / nuclear envelope / chromatin organization / protein-macromolecule adaptor activity / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / chromosome, telomeric region / ribonucleoprotein complex / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A.Z / Chromobox protein homolog 5 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human) / Xenopus laevis (African clawed frog) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsTan D / Sokolova V
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133611 United States
National Science Foundation (NSF, United States)1942049 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_42774.png

Downloads & links

-
Map

FileDownload / File: emd_42774.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map, consensus refinement with mask
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00551
Minimum - Maximum-0.00640711 - 0.026068319
Average (Standard dev.)0.00007597767 (±0.0011912591)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 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: Chromobox protein homolog 5
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.Z
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA Widom601 (208bp) strand1
    • DNA: DNA Widom601 (208bp) strand2

-
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: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 288 KDa

-
Macromolecule #1: Chromobox protein homolog 5

MacromoleculeName: Chromobox protein homolog 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.651398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSPEFGKKTK RTADSSSSED EEEYVVEKVL DRRVVKGQVE YLLKWKGFSE EHNTWEPEKN LDCPELISEF MKKYKKMKEG ENNKPREKS ESNKRKSNFS NSADDIKSKK KREQSNDIAR GFERGLEPEK IIGATDSCGD LMFLMKWKDT DEADLVLAKE A NVKCPQIV ...String:
GSPEFGKKTK RTADSSSSED EEEYVVEKVL DRRVVKGQVE YLLKWKGFSE EHNTWEPEKN LDCPELISEF MKKYKKMKEG ENNKPREKS ESNKRKSNFS NSADDIKSKK KREQSNDIAR GFERGLEPEK IIGATDSCGD LMFLMKWKDT DEADLVLAKE A NVKCPQIV IAFYEERLTW HAYPEDAENK EKETAKS

UniProtKB: Chromobox protein homolog 5

-
Macromolecule #2: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

-
Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

-
Macromolecule #4: Histone H2A.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.450601 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGGKAGKDSG KAKTKAVSRS QRAGLQFPVG RIHRHLKSRT TSHGRVGATA AVYSAAILEY LTAEVLELAG NASKDLKVKR ITPRHLQLA IRGDEELDSL IKATIAGGGV IPHIHKSLIG KKGQQKTV

UniProtKB: Histone H2A.Z

-
Macromolecule #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

-
Macromolecule #6: DNA Widom601 (208bp) strand1

MacromoleculeName: DNA Widom601 (208bp) strand1 / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 64.456039 KDa
SequenceString: (DA)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC) ...String:
(DA)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG) (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)(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)(DC)(DA)(DG)(DG)(DG)(DC) (DG) (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)(DT)

-
Macromolecule #7: DNA Widom601 (208bp) strand2

MacromoleculeName: DNA Widom601 (208bp) strand2 / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 63.988711 KDa
SequenceString: (DA)(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)(DC)(DG) (DC)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA) (DT) (DC)(DC)(DC)(DG)(DG)(DT) ...String:
(DA)(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)(DC)(DG) (DC)(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)(DC) (DA) (DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG)(DC)(DG)(DA)(DC)(DC)(DT)(DT) (DG)(DC)(DC)(DG)(DG)(DA)(DG)(DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
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 reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 74257
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)

-
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
Output model

PDB-8uxq:
Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome

+
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