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- EMDB-43554: In vitro reconstituted human chromatin -

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Basic information

Entry
Database: EMDB / ID: EMD-43554
TitleIn vitro reconstituted human chromatin
Map dataTomogram of in vitro reconsituted chromatin
Sample
  • Complex: In vitro reconstituted chromatin from human histones with a 3631 bp DNA sequence derived from the human ATOH1 gene
    • Complex: Histone Octamer
KeywordsChromatin structure / Polycomb / transcriptional regulation / repressive chromatin modifier / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsUckelmann M / Taveneau C / Levina V / Trepout S / de Marco A / Davidovich C
Funding support Australia, 5 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE210101669 Australia
Australian Research Council (ARC)DP190103407 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1162921 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1184637 Australia
National Health and Medical Research Council (NHMRC, Australia)APP2011767 Australia
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates.
Authors: Michael Uckelmann / Vita Levina / Cyntia Taveneau / Xiao Han Ng / Varun Pandey / Jasmine Martinez / Shweta Mendiratta / Justin Houx / Marion Boudes / Hari Venugopal / Sylvain Trépout / Alex ...Authors: Michael Uckelmann / Vita Levina / Cyntia Taveneau / Xiao Han Ng / Varun Pandey / Jasmine Martinez / Shweta Mendiratta / Justin Houx / Marion Boudes / Hari Venugopal / Sylvain Trépout / Alex J Fulcher / Qi Zhang / Sarena Flanigan / Minrui Li / Emma Sierecki / Yann Gambin / Partha Pratim Das / Oliver Bell / Alex de Marco / Chen Davidovich /
Abstract: The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial ...The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organization and dynamics of chromatin compacted by gene-repressing factors are unknown. Here, using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the polycomb repressive complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilized through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provide a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.
History
DepositionJan 30, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43554.png

Downloads & links

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Map

FileDownload / File: emd_43554.map.gz / Format: CCP4 / Size: 769 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of in vitro reconsituted chromatin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.52 Å/pix.
x 166 pix.
= 1082.32 Å		6.52 Å/pix.
x 1186 pix.
= 7732.72 Å		6.52 Å/pix.
x 1024 pix.
= 6676.48 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.52 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-96.275925000000001 - 79.844210000000004
Average (Standard dev.)1.062511 (±4.7556915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-9208-91
Dimensions11861024166
Spacing10241186166
CellA: 6676.48 Å / B: 7732.72 Å / C: 1082.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : In vitro reconstituted chromatin from human histones with a 3631 ...

EntireName: In vitro reconstituted chromatin from human histones with a 3631 bp DNA sequence derived from the human ATOH1 gene
Components
  • Complex: In vitro reconstituted chromatin from human histones with a 3631 bp DNA sequence derived from the human ATOH1 gene
    • Complex: Histone Octamer

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Supramolecule #1: In vitro reconstituted chromatin from human histones with a 3631 ...

SupramoleculeName: In vitro reconstituted chromatin from human histones with a 3631 bp DNA sequence derived from the human ATOH1 gene
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Histone Octamer

SupramoleculeName: Histone Octamer / type: complex / ID: 2 / Parent: 1
Details: Histone octamer from human histones H2A, H2B, H3, H4
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation state3D array

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
4.17 mMC8H18N2O4SHEPES ((4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid))
8.3 mMC4H11NO3Tris
25.0 mMNaClSodium Chloride
8.3 mMKClPotassium Chloride
1.0 mMC4H10O2S2Dithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerDiameter: 5 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 41 / Average electron dose: 3.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 53000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD (ver. 4.11.15) / Number images used: 41
CTF correctionSoftware - Name: IMOD (ver. 4.11.15)
Details: CTF correction was done on the final aligned stack. Defocus was estimated using emClarity and CTF correction was done in IMOD using the expected defocus from emClarity.
Type: PHASE FLIPPING ONLY

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