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- EMDB-42773: structure of the K9me3-H2A.Z nucleosome -

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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: 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_42773.png

Downloads & links

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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 °

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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: 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

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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: #1, #3-#6, #10-#11
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 288 MDa

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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

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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

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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

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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

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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

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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

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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
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 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)

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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

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