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- EMDB-34432: Cryo-EM structure of BAP1-ASXL1 bound to nucleosome -

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Entry
Database: EMDB / ID: EMD-34432
TitleCryo-EM structure of BAP1-ASXL1 bound to nucleosome
Map data
Sample
  • Complex: Cryo-EM structure of BAP1-ASXL1 bound to nucleosome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGe W / Yu C / Xu RM
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508900 China
National Natural Science Foundation of China (NSFC)31991162 China
National Natural Science Foundation of China (NSFC)918532204 China
National Natural Science Foundation of China (NSFC)92153302 China
CitationJournal: 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
DepositionOct 4, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34432.png

Downloads & links

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Map

FileDownload / File: emd_34432.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesX (Sec.)Y (Row.)Z (Col.)
1.04 Å/pix.
x 104 pix.
= 108.16 Å		1.04 Å/pix.
x 112 pix.
= 116.48 Å		1.04 Å/pix.
x 143 pix.
= 148.72 Å

Surface

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.04 Å
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Contour LevelBy AUTHOR: 0.072
Minimum - Maximum-1.3062178 - 1.5969126
Average (Standard dev.)-2.795551e-12 (±0.12061385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin726488
Dimensions112143104
Spacing104112143
CellA: 108.159996 Å / B: 116.479996 Å / C: 148.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34432_msk_1.map
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Additional map: #2

Fileemd_34432_additional_1.map
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Additional map: #1

Fileemd_34432_additional_2.map
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Half map: #1

Fileemd_34432_half_map_1.map
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Half map: #2

Fileemd_34432_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of BAP1-ASXL1 bound to nucleosome

EntireName: Cryo-EM structure of BAP1-ASXL1 bound to nucleosome
Components
  • Complex: Cryo-EM structure of BAP1-ASXL1 bound to nucleosome

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Supramolecule #1: Cryo-EM structure of BAP1-ASXL1 bound to nucleosome

SupramoleculeName: Cryo-EM structure of BAP1-ASXL1 bound to nucleosome / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#10
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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 284 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 3.2), RELION (ver. 3.0.8)) / Number images used: 56370
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: REAL

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