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- EMDB-9844: cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-9844
Titlecryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome
Map data
SampleDOT1L bound to H2B ubiquitinated nucleosome
  • nucleic-acidNucleic acid
  • Histone H3.2
  • Histone H4
  • Histone H2A
  • Histone H2B 1.1
  • Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
  • Ubiquitin
  • ligand
Function / homology
Function and homology information


histone methyltransferase activity (H3-K79 specific) / [histone H3]-lysine79 N-trimethyltransferase / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / hypothalamus gonadotrophin-releasing hormone neuron development / mitochondrion transport along microtubule / regulation of receptor signaling pathway via JAK-STAT / fat pad development / histone methyltransferase activity / female meiosis I ...histone methyltransferase activity (H3-K79 specific) / [histone H3]-lysine79 N-trimethyltransferase / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / hypothalamus gonadotrophin-releasing hormone neuron development / mitochondrion transport along microtubule / regulation of receptor signaling pathway via JAK-STAT / fat pad development / histone methyltransferase activity / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / male meiosis I / histone-lysine N-methyltransferase activity / chromatin silencing at telomere / female gonad development / seminiferous tubule development / regulation of neuron death / energy homeostasis / telomere organization / MyD88-independent toll-like receptor signaling pathway / nucleotide-excision repair, DNA gap filling / nucleotide-binding oligomerization domain containing signaling pathway / regulation of proteasomal protein catabolic process / nucleotide-excision repair, DNA damage recognition / regulation of mitochondrial membrane potential / nucleotide-excision repair, DNA duplex unwinding / TRIF-dependent toll-like receptor signaling pathway / DNA-templated transcription, initiation / positive regulation of protein ubiquitination / global genome nucleotide-excision repair / DNA damage checkpoint / nucleotide-excision repair, preincision complex assembly / neuron projection morphogenesis / endosomal transport / intracellular transport of virus / DNA damage response, detection of DNA damage / MyD88-dependent toll-like receptor signaling pathway / nucleotide-excision repair, DNA incision, 5'-to lesion / host cell / error-free translesion synthesis / nucleotide-excision repair, DNA incision / modification-dependent protein catabolic process / JNK cascade / protein targeting to peroxisome / chromosome, telomeric region / nucleosome / protein tag / stress-activated MAPK cascade / interstrand cross-link repair / endocytic vesicle membrane / error-prone translesion synthesis / interleukin-1-mediated signaling pathway / regulation of transcription from RNA polymerase II promoter in response to hypoxia / I-kappaB kinase/NF-kappaB signaling / viral life cycle / transcription-coupled nucleotide-excision repair / negative regulation of transforming growth factor beta receptor signaling pathway / translesion synthesis / transforming growth factor beta receptor signaling pathway / virion assembly / anaphase-promoting complex-dependent catabolic process / transmembrane transport / regulation of mRNA stability / membrane organization / protein polyubiquitination / Wnt signaling pathway / mitochondrial outer membrane / vesicle / activation of MAPK activity / endosome membrane / positive regulation of NF-kappaB transcription factor activity / protein ubiquitination / protein deubiquitination / protein heterodimerization activity / neuron projection / positive regulation of apoptotic process / intracellular membrane-bounded organelle / DNA repair / cytokine-mediated signaling pathway / transcription factor binding / neuronal cell body / endoplasmic reticulum membrane / cellular protein metabolic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / plasma membrane / nucleus / cytosol / cytoplasm
Histone H2B / Histone H3-K79 methyltransferase / Histone H4, conserved site / Ubiquitin conserved site / Ubiquitin domain / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / S-adenosyl-L-methionine-dependent methyltransferase / Ubiquitin-like domain superfamily / TATA box binding protein associated factor (TAF) ...Histone H2B / Histone H3-K79 methyltransferase / Histone H4, conserved site / Ubiquitin conserved site / Ubiquitin domain / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / S-adenosyl-L-methionine-dependent methyltransferase / Ubiquitin-like domain superfamily / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone H2A / Histone H4 / Ubiquitin-like domain / Histone H3/CENP-A / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / Histone-fold
Histone H2B 1.1 / Polyubiquitin-B / 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: 6.8 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: 6jma

SummaryFull reportAbout validation report
History
DepositionMar 7, 2019-
Header (metadata) releaseMay 15, 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: 0.0251
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0251
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jma
  • Surface level: 0.0251
  • 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_9844.map.gz / Format: CCP4 / Size: 40.6 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 220 pix.
= 233.2 Å
1.06 Å/pix.
x 220 pix.
= 233.2 Å
1.06 Å/pix.
x 220 pix.
= 233.2 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: 0.0251 / Movie #1: 0.0251
Minimum - Maximum-0.056371503 - 0.1053533
Average (Standard dev.)0.0010058607 (±0.0055386866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z233.200233.200233.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0560.1050.001

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Supplemental data

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Sample components

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Entire DOT1L bound to H2B ubiquitinated nucleosome

EntireName: DOT1L bound to H2B ubiquitinated nucleosome / Number of components: 9

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Component #1: protein, DOT1L bound to H2B ubiquitinated nucleosome

ProteinName: DOT1L bound to H2B ubiquitinated nucleosome / Recombinant expression: No
MassTheoretical: 290 kDa
SourceSpecies: Xenopus laevis (African clawed frog)

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Component #2: nucleic-acid, DNA I&J

nucleic acidName: DNA I&J / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)
MassTheoretical: 35.168547 kDa
SourceSpecies: synthetic construct (others)

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Component #3: 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 #4: 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 #5: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 12.660719 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #6: 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 #7: 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 #8: protein, Ubiquitin

ProteinName: Ubiquitin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.576831 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: 122242
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Output model

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