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- EMDB-9783: Cryo-EM structure of human DOT1L in complex with an H2B-monoubiqu... -

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Entry
Database: EMDB / ID: 9783
TitleCryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome
Map dataThe main map for the overall structure of human DOT1L-ubNCP complex
SampleHuman DOT1L in complex with an H2B-monoubiquitinated nucleosome
  • Histone H3
  • Histone H4
  • Histone H2A
  • Histone H2B 1.1
  • (nucleic-acidNucleic acid) x 2
  • Ubiquitin
  • Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
  • ligand
Function / homologyVif-mediated degradation of APOBEC3G / Membrane binding and targetting of GAG proteins / Budding and maturation of HIV virion / NOD1/2 Signaling Pathway / TICAM1, RIP1-mediated IKK complex recruitment / DDX58/IFIH1-mediated induction of interferon-alpha/beta / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin ...Vif-mediated degradation of APOBEC3G / Membrane binding and targetting of GAG proteins / Budding and maturation of HIV virion / NOD1/2 Signaling Pathway / TICAM1, RIP1-mediated IKK complex recruitment / DDX58/IFIH1-mediated induction of interferon-alpha/beta / APC/C:Cdc20 mediated degradation of Cyclin B / 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 / Assembly Of The HIV Virion / L13a-mediated translational silencing of Ceruloplasmin expression / APC-Cdc20 mediated degradation of Nek2A / SRP-dependent cotranslational protein targeting to membrane / Vpu mediated degradation of CD4 / TNFR2 non-canonical NF-kB pathway / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Viral mRNA Translation / 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 / Peptide chain elongation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Histone H2B signature. / Core histone H2A/H2B/H3/H4 / Ubiquitin family / Ribosomal protein S27a / Histone methylation protein DOT1 / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone H2A signature. / Histone H4 signature. / Ubiquitin domain signature. / Histone H3 signature 1. / Histone H3 signature 2. / Spry regulation of FGF signaling / Ubiquitin domain profile. / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / Translesion synthesis by REV1 / 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 / p75NTR recruits signalling complexes / Regulation of activated PAK-2p34 by proteasome mediated degradation / CENP-T/Histone H4, histone fold / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / AUF1 (hnRNP D0) binds and destabilizes mRNA / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / 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 / Dectin-1 mediated noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Selenocysteine synthesis / Separation of Sister Chromatids / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Regulation of PLK1 Activity at G2/M Transition / Stimuli-sensing channels / Circadian Clock / Constitutive Signaling by NOTCH1 HD Domain Mutants / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus
Function and homology information
SourceAfrican clawed frog (African clawed frog) / Human (human) / Xenopus laevis (African clawed frog) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsYao T / Huang J
CitationJournal: Cell Res. / Year: 2019
Title: Structural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome.
Authors: Tonghui Yao / Wei Jing / Zhiguo Hu / Ming Tan / Mi Cao / Qianmin Wang / Yan Li / Guiyong Yuan / Ming Lei / Jing Huang
Validation ReportPDB-ID: 6j99

SummaryFull reportAbout validation report
DateDeposition: Jan 22, 2019 / Header (metadata) release: Feb 27, 2019 / Map release: Feb 27, 2019 / Last update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6j99
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9783.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.3 Å/pix.
= 260. Å
200 pix
1.3 Å/pix.
= 260. Å
200 pix
1.3 Å/pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.028 (by author), 0.028 (movie #1):
Minimum - Maximum-0.14869481 - 0.25374833
Average (Standard dev.)-0.00034746548 (0.009964193)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 260.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z260.000260.000260.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1490.254-0.000

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Supplemental data

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Mask #1

Fileemd_9783_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Human DOT1L in complex with an H2B-monoubiquitinated nucleosome

EntireName: Human DOT1L in complex with an H2B-monoubiquitinated nucleosome
Number of components: 12

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Component #1: protein, Human DOT1L in complex with an H2B-monoubiquitinated nuc...

ProteinName: Human DOT1L in complex with an H2B-monoubiquitinated nucleosome
Recombinant expression: No
MassTheoretical: 250 kDa
SourceSpecies: African clawed frog (African clawed frog)

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Component #2: protein, Human DOT1L in complex with an H2B-monoubiquitinated nuc...

ProteinName: Human DOT1L in complex with an H2B-monoubiquitinated nucleosome
Recombinant expression: No
SourceSpecies: Human (human)

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Component #3: protein, Human DOT1L in complex with an H2B-monoubiquitinated nuc...

ProteinName: Human DOT1L in complex with an H2B-monoubiquitinated nucleosome
Recombinant expression: No

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Component #4: protein, Histone H3

ProteinName: Histone H3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.435126 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.109436 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.629911 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: nucleic-acid, DNA (144-MER)

Nucleic-acidName: DNA (144-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT)
MassTheoretical: 45.13877 kDa
SourceSpecies: synthetic construct (others)

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Component #9: nucleic-acid, DNA (145-MER)

Nucleic-acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DG)(DA)(DT)
MassTheoretical: 45.610043 kDa
SourceSpecies: synthetic construct (others)

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Component #10: protein, Ubiquitin

ProteinName: Ubiquitin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.622922 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, Histone-lysine N-methyltransferase, H3 lysine-79 specific

ProteinName: Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
Details: S-ADENOSYL-L-HOMOCYSTEINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.506156 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: ligand, S-ADENOSYL-L-HOMOCYSTEINE

LigandName: S-ADENOSYL-L-HOMOCYSTEINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.384411 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.98 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: 151545
3D reconstructionResolution: 4.1 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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