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- EMDB-33139: cryo-EM map of Dot1L and H3K79Nle nucleosome complex (active state) -

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Basic information

Entry
Database: EMDB / ID: EMD-33139
Titlecryo-EM map of Dot1L and H3K79Nle nucleosome complex (active state)
Map data
Sample
  • Complex: Complex of Dot1L(1-416) and H3K79Nle nucleosome (active state)
KeywordsDot1L / Nucleosome / H3K79Nle / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsAi HS / Liu AJ / Lou ZY / Liu L
Funding support China, 5 items
OrganizationGrant numberCountry
Other private2017YFA0505200
National Natural Science Foundation of China (NSFC)21977090 China
National Natural Science Foundation of China (NSFC)21532004 China
National Natural Science Foundation of China (NSFC)91753205 China
National Natural Science Foundation of China (NSFC)81621002 China
CitationJournal: Nat Chem Biol / Year: 2022
Title: H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity.
Authors: Huasong Ai / Maoshen Sun / Aijun Liu / Zixian Sun / Tingting Liu / Lin Cao / Lujun Liang / Qian Qu / Zichen Li / Zhiheng Deng / Zebin Tong / Guochao Chu / Xiaolin Tian / Haiteng Deng / Suwen ...Authors: Huasong Ai / Maoshen Sun / Aijun Liu / Zixian Sun / Tingting Liu / Lin Cao / Lujun Liang / Qian Qu / Zichen Li / Zhiheng Deng / Zebin Tong / Guochao Chu / Xiaolin Tian / Haiteng Deng / Suwen Zhao / Jia-Bin Li / Zhiyong Lou / Lei Liu /
Abstract: Ubiquitination-dependent histone crosstalk plays critical roles in chromatin-associated processes and is highly associated with human diseases. Mechanism studies of the crosstalk have been of the ...Ubiquitination-dependent histone crosstalk plays critical roles in chromatin-associated processes and is highly associated with human diseases. Mechanism studies of the crosstalk have been of the central focus. Here our study on the crosstalk between H2BK34ub and Dot1L-catalyzed H3K79me suggests a novel mechanism of ubiquitination-induced nucleosome distortion to stimulate the activity of an enzyme. We determined the cryo-electron microscopy structures of Dot1L-H2BK34ub nucleosome complex and the H2BK34ub nucleosome alone. The structures reveal that H2BK34ub induces an almost identical orientation and binding pattern of Dot1L on nucleosome as H2BK120ub, which positions Dot1L for the productive conformation through direct ubiquitin-enzyme contacts. However, H2BK34-anchored ubiquitin does not directly interact with Dot1L as occurs in the case of H2BK120ub, but rather induces DNA and histone distortion around the modified site. Our findings establish the structural framework for understanding the H2BK34ub-H3K79me trans-crosstalk and highlight the diversity of mechanisms for histone ubiquitination to activate chromatin-modifying enzymes.
History
DepositionMar 26, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33139.png

Downloads & links

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Map

FileDownload / File: emd_33139.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0979 Å
Density
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.10173443 - 0.18816142
Average (Standard dev.)0.00013262278 (±0.004023519)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.0624 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33139_msk_1.map
Projections & Slices
AxesZYX

Projections

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Additional map: #1

Fileemd_33139_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_33139_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33139_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Complex of Dot1L(1-416) and H3K79Nle nucleosome (active state)

EntireName: Complex of Dot1L(1-416) and H3K79Nle nucleosome (active state)
Components
  • Complex: Complex of Dot1L(1-416) and H3K79Nle nucleosome (active state)

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Supramolecule #1: Complex of Dot1L(1-416) and H3K79Nle nucleosome (active state)

SupramoleculeName: Complex of Dot1L(1-416) and H3K79Nle nucleosome (active state)
type: complex / ID: 1 / Parent: 0
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 572840

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