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- EMDB-34957: Cryo-EM structure of H2AK119Ub nucleosome at a resolution of 6.11... -

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Basic information

Entry
Database: EMDB / ID: EMD-34957
TitleCryo-EM structure of H2AK119Ub nucleosome at a resolution of 6.11 angstrom
Map data
Sample
  • Complex: the H2AK119Ub nucleosome
KeywordsH2AK119Ub nucleosome / PRC1 / SSX1 / Synovial Sarcoma / ssBAF / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.11 Å
AuthorsZebin T / Ai HS / Ziyu X / Man P / Liu L
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302 China
Other government2022TQ0170, 2022M720075 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Synovial sarcoma X breakpoint 1 protein uses a cryptic groove to selectively recognize H2AK119Ub nucleosomes.
Authors: Zebin Tong / Huasong Ai / Ziyu Xu / Kezhang He / Guo-Chao Chu / Qiang Shi / Zhiheng Deng / Qiaomei Xue / Maoshen Sun / Yunxiang Du / Lujun Liang / Jia-Bin Li / Man Pan / Lei Liu /
Abstract: The cancer-specific fusion oncoprotein SS18-SSX1 disturbs chromatin accessibility by hijacking the BAF complex from the promoters and enhancers to the Polycomb-repressed chromatin regions. This ...The cancer-specific fusion oncoprotein SS18-SSX1 disturbs chromatin accessibility by hijacking the BAF complex from the promoters and enhancers to the Polycomb-repressed chromatin regions. This process relies on the selective recognition of H2AK119Ub nucleosomes by synovial sarcoma X breakpoint 1 (SSX1). However, the mechanism underlying the selective recognition of H2AK119Ub nucleosomes by SSX1 in the absence of ubiquitin (Ub)-binding capacity remains unknown. Here we report the cryo-EM structure of SSX1 bound to H2AK119Ub nucleosomes at 3.1-Å resolution. Combined in vitro biochemical and cellular assays revealed that the Ub recognition by SSX1 is unique and depends on a cryptic basic groove formed by H3 and the Ub motif on the H2AK119 site. Moreover, this unorthodox binding mode of SSX1 induces DNA unwrapping at the entry/exit sites. Together, our results describe a unique mode of site-specific ubiquitinated nucleosome recognition that underlies the specific hijacking of the BAF complex to Polycomb regions by SS18-SSX1 in synovial sarcoma.
History
DepositionDec 14, 2022-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34957.png

Downloads & links

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Map

FileDownload / File: emd_34957.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0033159768 - 0.018765073
Average (Standard dev.)0.0003032004 (±0.0014860056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.016 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_34957_additional_1.map
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Half map: #1

Fileemd_34957_half_map_1.map
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Half map: #2

Fileemd_34957_half_map_2.map
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Sample components

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Entire : the H2AK119Ub nucleosome

EntireName: the H2AK119Ub nucleosome
Components
  • Complex: the H2AK119Ub nucleosome

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Supramolecule #1: the H2AK119Ub nucleosome

SupramoleculeName: the H2AK119Ub nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 220 KDa

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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

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Electron microscopy

MicroscopeFEI TALOS 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23536
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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