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Yorodumi- EMDB-35180: Constituent map of cryo-EM structure of BAP1-ASXL1 bound to chrom... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35180 | |||||||||||||||
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Title | Constituent map of cryo-EM structure of BAP1-ASXL1 bound to chromatosome | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | Ge W / Yu C / Xu RM | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Nature / Year: 2023 Title: Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase. Authors: Weiran Ge / Cong Yu / Jingjing Li / Zhenyu Yu / Xiaorong Li / Yan Zhang / Chao-Pei Liu / Yingfeng Li / Changlin Tian / Xinzheng Zhang / Guohong Li / Bing Zhu / Rui-Ming Xu / Abstract: Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification. The Polycomb repressive ...Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification. The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119ub1) on the nucleosome, counteracting the ubiquitin E3 ligase activity of Polycomb repressive complex 1 (PRC1) to facilitate the correct silencing of genes by Polycomb proteins and safeguard active genes from inadvertent silencing by PRC1 (refs. ). The intricate biological function of PR-DUB requires accurate targeting of H2AK119ub1, but PR-DUB can deubiquitinate monoubiquitinated free histones and peptide substrates indiscriminately; the basis for its exquisite nucleosome-dependent substrate specificity therefore remains unclear. Here we report the cryo-electron microscopy structure of human PR-DUB, composed of BAP1 and ASXL1, in complex with the chromatosome. We find that ASXL1 directs the binding of the positively charged C-terminal extension of BAP1 to nucleosomal DNA and histones H3-H4 near the dyad, an addition to its role in forming the ubiquitin-binding cleft. Furthermore, a conserved loop segment of the catalytic domain of BAP1 is situated near the H2A-H2B acidic patch. This distinct nucleosome-binding mode displaces the C-terminal tail of H2A from the nucleosome surface, and endows PR-DUB with the specificity for H2AK119ub1. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35180.map.gz | 157 MB | EMDB map data format | |
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Header (meta data) | emd-35180-v30.xml emd-35180.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35180_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_35180.png | 122.9 KB | ||
Others | emd_35180_half_map_1.map.gz emd_35180_half_map_2.map.gz | 154.6 MB 154.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35180 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35180 | HTTPS FTP |
-Validation report
Summary document | emd_35180_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_35180_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_35180_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | emd_35180_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35180 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35180 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35180.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35180_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35180_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Entire | Name: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome |
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Components |
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-Supramolecule #1: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Supramolecule | Name: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#10 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 284 K |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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