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- EMDB-42774: Structure of Heterochromatin Protein 1 (HP1) alpha in complex wit... -

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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 / nucleosomal DNA binding / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding ...chromocenter / nucleosomal DNA binding / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / : / transcription repressor complex / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by KRAB-ZFP proteins / cellular response to estradiol stimulus / euchromatin / kinetochore / histone deacetylase binding / structural constituent of chromatin / nucleosome / nuclear envelope / heterochromatin formation / nucleosome assembly / chromatin organization / Factors involved in megakaryocyte development and platelet production / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / ribonucleoprotein complex / 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 / 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 / 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: Structure / Year: 2024
Title: Structural mechanism of HP1⍺-dependent transcriptional repression and chromatin compaction.
Authors: Vladyslava Sokolova / Jacob Miratsky / Vladimir Svetlov / Michael Brenowitz / John Vant / Tyler S Lewis / Kelly Dryden / Gahyun Lee / Shayan Sarkar / Evgeny Nudler / Abhishek Singharoy / Dongyan Tan /
Abstract: Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their ...Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. Here, we present the cryoelectron microscopy (cryo-EM) structure of an HP1α dimer bound to an H2A.Z-nucleosome, revealing two distinct HP1α-nucleosome interfaces. The primary HP1α binding site is located at the N terminus of histone H3, specifically at the trimethylated lysine 9 (K9me3) region, while a secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. Our study offers a model for HP1α-mediated heterochromatin maintenance and gene silencing. It also sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
History
DepositionNov 9, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42774.png

Downloads & links

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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 °

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Supplemental data

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Sample components

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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

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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

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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

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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

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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

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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

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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

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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)

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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)

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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
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

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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

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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)

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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

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