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- EMDB-40791: Overall map of BAP1/ASXL1 bound to the H2AK119Ub Nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-40791
TitleOverall map of BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Map dataOverall map of BAP1/ASXL1 bound to the H2AK119Ub nucleosome
Sample
  • Complex: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
KeywordsDNA complex protein / hydrolase / structural protein / NUCLEAR PROTEIN-DNA complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsThomas JF / Valencia-Sanchez MI
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115882 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA266978 United States
The Mark Foundation United States
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1.
Authors: Jonathan F Thomas / Marco Igor Valencia-Sánchez / Simone Tamburri / Susan L Gloor / Samantha Rustichelli / Victoria Godínez-López / Pablo De Ioannes / Rachel Lee / Stephen Abini-Agbomson ...Authors: Jonathan F Thomas / Marco Igor Valencia-Sánchez / Simone Tamburri / Susan L Gloor / Samantha Rustichelli / Victoria Godínez-López / Pablo De Ioannes / Rachel Lee / Stephen Abini-Agbomson / Kristjan Gretarsson / Jonathan M Burg / Allison R Hickman / Lu Sun / Saarang Gopinath / Hailey F Taylor / Zu-Wen Sun / Ryan J Ezell / Anup Vaidya / Matthew J Meiners / Marcus A Cheek / William J Rice / Vladimir Svetlov / Evgeny Nudler / Chao Lu / Michael-Christopher Keogh / Diego Pasini / Karim-Jean Armache /
Abstract: Histone H2A lysine 119 (H2AK119Ub) is monoubiquitinated by Polycomb repressive complex 1 and deubiquitinated by Polycomb repressive deubiquitinase complex (PR-DUB). PR-DUB cleaves H2AK119Ub to ...Histone H2A lysine 119 (H2AK119Ub) is monoubiquitinated by Polycomb repressive complex 1 and deubiquitinated by Polycomb repressive deubiquitinase complex (PR-DUB). PR-DUB cleaves H2AK119Ub to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. The PR-DUB subunits (BAP1 and ASXL1) are among the most frequently mutated epigenetic factors in human cancers. How PR-DUB establishes specificity for H2AK119Ub over other nucleosomal ubiquitination sites and how disease-associated mutations of the enzyme affect activity are unclear. Here, we determine a cryo-EM structure of human BAP1 and the ASXL1 DEUBAD in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for restructuring the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing insight into understanding cancer etiology.
History
DepositionMay 16, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40791.png

Downloads & links

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Map

FileDownload / File: emd_40791.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map of BAP1/ASXL1 bound to the H2AK119Ub nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 316.125 Å		1.05 Å/pix.
x 300 pix.
= 316.125 Å		1.05 Å/pix.
x 300 pix.
= 316.125 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.5044036 - 1.4530647
Average (Standard dev.)0.0029734266 (±0.051614128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 316.125 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40791_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened overall map of BAP1/ASXL1 bound to the H2AK119Ub nucleosome

Fileemd_40791_additional_1.map
AnnotationSharpened overall map of BAP1/ASXL1 bound to the H2AK119Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of overall of BAP1/ASXL1 bound to the H2AK119Ub nucleosome

Fileemd_40791_half_map_1.map
AnnotationHalf map B of overall of BAP1/ASXL1 bound to the H2AK119Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of overall of BAP1/ASXL1 bound to the H2AK119Ub nucleosome

Fileemd_40791_half_map_2.map
AnnotationHalf map A of overall of BAP1/ASXL1 bound to the H2AK119Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BAP1/ASXL1 bound to the H2AK119Ub Nucleosome

EntireName: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Components
  • Complex: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome

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Supramolecule #1: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome

SupramoleculeName: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.12 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 17986
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: AlphaFold, initial_model_type: in silico modelMultimer prediction
source_name: PDB, initial_model_type: experimental model

3tu4

source_name: Other, initial_model_type: integrative modelSwissModel template

4uel

source_name: Other, initial_model_type: integrative modelSwissModel template

6hgc

source_name: PDB, initial_model_type: experimental model

7k5y

RefinementSpace: REAL

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