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- EMDB-32094: Cryo-EM structure of H2A-ubiquitinated nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-32094
TitleCryo-EM structure of H2A-ubiquitinated nucleosome
Map data
Sample
  • Complex: modified nucleosome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsOhtomo H / Ito S / McKenzie NJ / Uckelmann M / Wakamori M / Ehara H / Tsunaka Y / Shibata M / Sekine S / Umehara T ...Ohtomo H / Ito S / McKenzie NJ / Uckelmann M / Wakamori M / Ehara H / Tsunaka Y / Shibata M / Sekine S / Umehara T / Davidovich C / Koseki H / Nishimura Y
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: J Mol Biol / Year: 2023
Title: H2A Ubiquitination Alters H3-tail Dynamics on Linker-DNA to Enhance H3K27 Methylation.
Authors: Hideaki Ohtomo / Shinsuke Ito / Nicholas J McKenzie / Michael Uckelmann / Masatoshi Wakamori / Haruhiko Ehara / Ayako Furukawa / Yasuo Tsunaka / Marika Shibata / Shun-Ichi Sekine / Takashi ...Authors: Hideaki Ohtomo / Shinsuke Ito / Nicholas J McKenzie / Michael Uckelmann / Masatoshi Wakamori / Haruhiko Ehara / Ayako Furukawa / Yasuo Tsunaka / Marika Shibata / Shun-Ichi Sekine / Takashi Umehara / Chen Davidovich / Haruhiko Koseki / Yoshifumi Nishimura /
Abstract: Polycomb repressive complex 1 (PRC1) and PRC2 are responsible for epigenetic gene regulation. PRC1 ubiquitinates histone H2A (H2Aub), which subsequently promotes PRC2 to introduce the H3 lysine 27 ...Polycomb repressive complex 1 (PRC1) and PRC2 are responsible for epigenetic gene regulation. PRC1 ubiquitinates histone H2A (H2Aub), which subsequently promotes PRC2 to introduce the H3 lysine 27 tri-methyl (H3K27me3) repressive chromatin mark. Although this mechanism provides a link between the two key transcriptional repressors, PRC1 and PRC2, it is unknown how histone-tail dynamics contribute to this process. Here, we have examined the effect of H2A ubiquitination and linker-DNA on H3-tail dynamics and H3K27 methylation by PRC2. In naïve nucleosomes, the H3-tail dynamically contacts linker DNA in addition to core DNA, and the linker-DNA is as important for H3K27 methylation as H2A ubiquitination. H2A ubiquitination alters contacts between the H3-tail and DNA to improve the methyltransferase activity of the PRC2-AEBP2-JARID2 complex. Collectively, our data support a model in which H2A ubiquitination by PRC1 synergizes with linker-DNA to hold H3 histone tails poised for their methylation by PRC2-AEBP2-JARID2.
History
DepositionOct 21, 2021-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32094.png

Downloads & links

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Map

FileDownload / File: emd_32094.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.47 Å
Density
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.027351003 - 0.08239146
Average (Standard dev.)0.00020024682 (±0.004662793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 235.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_32094_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32094_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : modified nucleosome

EntireName: modified nucleosome
Components
  • Complex: modified nucleosome

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Supramolecule #1: modified nucleosome

SupramoleculeName: modified nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration2 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
25.0 mMMES2-(N-morpholino)ethanesulfonic acid
25.0 mMKClpotassium chloride
2.0 mMDTTdithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 23630
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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