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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


APC/C:Cdc20 mediated degradation of Cyclin B / Budding and maturation of HIV virion / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / ISG15 antiviral mechanism / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / ER-Phagosome pathway / Downregulation of ERBB4 signaling ...APC/C:Cdc20 mediated degradation of Cyclin B / Budding and maturation of HIV virion / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / ISG15 antiviral mechanism / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / ER-Phagosome pathway / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / TICAM1, RIP1-mediated IKK complex recruitment / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Negative regulation of FGFR1 signaling / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / APC-Cdc20 mediated degradation of Nek2A / Translesion synthesis by REV1 / Vif-mediated degradation of APOBEC3G / Vpu mediated degradation of CD4 / EGFR downregulation / Degradation of AXIN / Autodegradation of the E3 ubiquitin ligase COP1 / Deactivation of the beta-catenin transactivating complex / Myoclonic epilepsy of Lafora / ABC-family proteins mediated transport / Circadian Clock / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Asymmetric localization of PCP proteins / Degradation of DVL / PKMTs methylate histone lysines / Regulation of FZD by ubiquitination / Pink/Parkin Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NFkappaB signaling pathway / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / Glycogen synthesis / Regulation of innate immune responses to cytosolic DNA / SCF(Skp2)-mediated degradation of p27/p21 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / Downstream TCR signaling / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Regulation of activated PAK-2p34 by proteasome mediated degradation / NOTCH1 Intracellular Domain Regulates Transcription / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / NOTCH2 Activation and Transmission of Signal to the Nucleus / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Separation of Sister Chromatids / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Regulation of PLK1 Activity at G2/M Transition / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Stimuli-sensing channels / Constitutive Signaling by NOTCH1 HD Domain Mutants / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Hedgehog 'on' state / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / InlA-mediated entry of Listeria monocytogenes into host cells / InlB-mediated entry of Listeria monocytogenes into host cell / E3 ubiquitin ligases ubiquitinate target proteins / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Downregulation of ERBB2 signaling / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PTEN localization / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / G2/M Checkpoints / Cyclin D associated events in G1 / rt:r-hsa-69229: / CDK-mediated phosphorylation and removal of Cdc6 / Orc1 removal from chromatin
Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / Ubiquitin domain profile. / CENP-T/Histone H4, histone fold / Ubiquitin conserved site / Ubiquitin / Polyketide synthase, enoylreductase domain / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / S-adenosyl-L-methionine-dependent methyltransferase / Ubiquitin-like domain superfamily ...Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / Ubiquitin domain profile. / CENP-T/Histone H4, histone fold / Ubiquitin conserved site / Ubiquitin / Polyketide synthase, enoylreductase domain / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / S-adenosyl-L-methionine-dependent methyltransferase / Ubiquitin-like domain superfamily / Histone H3-K79 methyltransferase / Histone H2A, C-terminal domain / Histone H2A conserved site / NAD(P)-binding domain superfamily / Histone H2B signature. / Zinc-binding dehydrogenase / Core histone H2A/H2B/H3/H4 / Ubiquitin family / Histone methylation protein DOT1 / Alcohol dehydrogenase GroES-like domain / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone H2A signature. / Histone H4 signature. / Zinc-containing alcohol dehydrogenases signature. / Ubiquitin domain signature. / Alcohol dehydrogenase, N-terminal / Histone H4, conserved site / Alcohol dehydrogenase, C-terminal / GroES-like superfamily / Histone H2B / Ubiquitin domain / Histone H4 / Histone H2A / Alcohol dehydrogenase, zinc-type, conserved site / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold
Histone H2B 1.1 / Polyubiquitin-B / Histone H4 / Nerol dehydrogenase / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-79 specific
SourceXenopus laevis (African clawed frog) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsJang S / Song JJ
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
DateDeposition: Mar 7, 2019 / Header (metadata) release: May 15, 2019 / Map release: May 15, 2019 / Update: May 22, 2019

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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)(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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