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Yorodumi- EMDB-34957: Cryo-EM structure of H2AK119Ub nucleosome at a resolution of 6.11... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34957 | |||||||||
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Title | Cryo-EM structure of H2AK119Ub nucleosome at a resolution of 6.11 angstrom | |||||||||
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Sample |
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Keywords | H2AK119Ub nucleosome / PRC1 / SSX1 / Synovial Sarcoma / ssBAF / STRUCTURAL PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.11 Å | |||||||||
Authors | Zebin T / Ai HS / Ziyu X / Man P / Liu L | |||||||||
Funding support | China, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34957.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-34957-v30.xml emd-34957.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_34957.png | 28.9 KB | ||
Filedesc metadata | emd-34957.cif.gz | 4 KB | ||
Others | emd_34957_additional_1.map.gz emd_34957_half_map_1.map.gz emd_34957_half_map_2.map.gz | 49.1 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34957 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34957 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34957.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.836 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_34957_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_34957_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_34957_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the H2AK119Ub nucleosome
Entire | Name: the H2AK119Ub nucleosome |
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Components |
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-Supramolecule #1: the H2AK119Ub nucleosome
Supramolecule | Name: the H2AK119Ub nucleosome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 220 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23536 |