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- EMDB-9843: cryo-EM structure of DOT1L bound to unmodified nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-9843
Titlecryo-EM structure of DOT1L bound to unmodified nucleosome
Map data
SampleDOT1L bound to unmodified nucleosome
  • (nucleic-acidNucleic acid) x 2
  • Histone H3.2
  • Histone H4
  • Histone H2A
  • Histone H2B 1.1
  • Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
  • ligand
Function / homology
Function and homology information


[histone H3]-lysine79 N-trimethyltransferase / histone methyltransferase activity (H3-K79 specific) / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / histone-lysine N-methyltransferase activity / chromatin silencing at telomere / telomere organization / DNA-templated transcription, initiation ...[histone H3]-lysine79 N-trimethyltransferase / histone methyltransferase activity (H3-K79 specific) / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / histone-lysine N-methyltransferase activity / chromatin silencing at telomere / telomere organization / DNA-templated transcription, initiation / DNA damage checkpoint / chromosome, telomeric region / nucleosome / protein heterodimerization activity / intracellular membrane-bounded organelle / DNA repair / transcription factor binding / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus
TATA box binding protein associated factor (TAF) / Histone H3-K79 methyltransferase, metazoa / Histone H2A / Histone H4 / CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Histone H3-K79 methyltransferase / Histone H2B / Histone H3/CENP-A ...TATA box binding protein associated factor (TAF) / Histone H3-K79 methyltransferase, metazoa / Histone H2A / Histone H4 / CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Histone H3-K79 methyltransferase / Histone H2B / Histone H3/CENP-A / S-adenosyl-L-methionine-dependent methyltransferase / Histone-lysine N-methyltransferase DOT1 domain / Histone-fold / Histone H4, conserved site / Histone H2A/H2B/H3
Histone H2B 1.1 / Histone H4 / Histone H3.2 / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Biological speciesXenopus laevis (African clawed frog) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsJang S / Song JJ
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016R1A2B3006293 Korea, Republic Of
National Research Foundation (Korea)NRF- 2016H1A2A1908806 Korea, Republic Of
National Research Foundation (Korea)NRF-2016K1A1A2912057 Korea, Republic Of
CitationJournal: Genes Dev. / Year: 2019
Title: Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase.
Authors: Seongmin Jang / Chanshin Kang / Han-Sol Yang / Taeyang Jung / Hans Hebert / Ka Young Chung / Seung Joong Kim / Sungchul Hohng / Ji-Joon Song /
Abstract: DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we ...DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Furthermore, the structures combined with single-molecule FRET experiments show that H2B ubiquitination enhances a noncatalytic function of the DOT1L-destabilizing nucleosome. These results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L.
Validation ReportPDB-ID: 6jm9

SummaryFull reportAbout validation report
History
DepositionMar 7, 2019-
Header (metadata) releaseMar 20, 2019-
Map releaseMay 15, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jm9
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9843.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å
1.06 Å/pix.
x 200 pix.
= 212. Å
1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.021 / Movie #1: 0.021
Minimum - Maximum-0.023256859 - 0.08723088
Average (Standard dev.)0.001189177 (±0.0059938785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0230.0870.001

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Supplemental data

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Sample components

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Entire DOT1L bound to unmodified nucleosome

EntireName: DOT1L bound to unmodified nucleosome / Number of components: 9

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Component #1: protein, DOT1L bound to unmodified nucleosome

ProteinName: DOT1L bound to unmodified nucleosome / Recombinant expression: No
MassTheoretical: 270 kDa
SourceSpecies: Xenopus laevis (African clawed frog)

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Component #2: nucleic-acid, DNA strand I

nucleic acidName: DNA strand IDNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA) (DT)(DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG)(DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT)(DC) (DC)(DA)(DT)(DC)(DA)(DA) ...Sequence:
(DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA) (DT)(DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG)(DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT)(DC) (DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG) (DC)(DA)(DT)(DG)(DT)(DT)(DC)(DA)(DG)(DC) (DT)(DG)(DA)(DA)(DT)(DT)(DC)(DA)(DG)(DC) (DT)(DG)(DA)(DA)(DC)(DA)(DT)(DG)(DC)(DC) (DT)(DT)(DT)(DT)(DG)(DA)(DT)(DG)(DG)(DA) (DG)(DC)(DA)(DG)(DT)(DT)(DT)(DC)(DC)(DA) (DA)(DA)(DT)(DA)(DC)(DA)(DC)(DT)(DT)(DT) (DT)(DG)(DG)(DT)(DA)(DG)(DA)(DA)(DT)(DC) (DT)(DG)(DC)
MassTheoretical: 37.890262 kDa
SourceSpecies: synthetic construct (others)

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Component #3: nucleic-acid, DNA strand J

nucleic acidName: DNA strand J / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DG)(DC)(DA)(DG)(DA)(DT)(DT)(DC)(DT)(DA) (DC)(DC)(DA)(DA)(DA)(DA)(DG)(DT)(DG)(DT) (DA)(DT)(DT)(DT)(DG)(DG)(DA)(DA)(DA)(DC) (DT)(DG)(DC)(DT)(DC)(DC)(DA)(DT)(DC)(DA) (DA)(DA)(DA)(DG)(DG)(DC) ...Sequence:
(DG)(DC)(DA)(DG)(DA)(DT)(DT)(DC)(DT)(DA) (DC)(DC)(DA)(DA)(DA)(DA)(DG)(DT)(DG)(DT) (DA)(DT)(DT)(DT)(DG)(DG)(DA)(DA)(DA)(DC) (DT)(DG)(DC)(DT)(DC)(DC)(DA)(DT)(DC)(DA) (DA)(DA)(DA)(DG)(DG)(DC)(DA)(DT)(DG)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DA)(DA)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DA)(DA)(DC) (DA)(DT)(DG)(DC)(DC)(DT)(DT)(DT)(DT)(DG) (DA)(DT)(DG)(DG)(DA)(DG)(DC)(DA)(DG)(DT) (DT)(DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC) (DA)(DC)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DA) (DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DG)
MassTheoretical: 38.01034 kDa
SourceSpecies: synthetic construct (others)

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Component #4: protein, Histone H3.2

ProteinName: Histone H3.2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.48841 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.99077 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #6: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.724677 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #7: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.478032 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #8: protein, Histone-lysine N-methyltransferase, H3 lysine-79 specific

ProteinName: Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.930039 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #9: ligand, S-ADENOSYLMETHIONINE

LigandName: S-ADENOSYLMETHIONINES-Adenosyl methionine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.398437 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 37.28 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 21229
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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