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- PDB-6j99: Cryo-EM structure of human DOT1L in complex with an H2B-monoubiqu... -

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Entry
Database: PDB / ID: 6j99
TitleCryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome
Components
  • DNA (144-MER)
  • DNA (145-MER)
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
  • Ubiquitin
KeywordsTRANSCRIPTION / epigenetics / nucleosome / DOT1L / histone modification
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
Specimen sourceXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsYao, T. / Huang, J.
Funding supportChina , 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501803China
National Natural Science Foundation of China31570766China
National Natural Science Foundation of ChinaU1632130China
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jan 22, 2019 / Release: Feb 27, 2019

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Structure visualization

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (144-MER)
J: DNA (145-MER)
L: Ubiquitin
K: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,40013
Polyers256,01612
Non-polymers3841
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)61880
ΔGint (kcal/M)-385
Surface area (Å2)89180

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Components

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Protein/peptide , 6 types, 10 molecules AEBFCGDHLK

#1: Protein/peptide Histone H3 /


Mass: 15435.126 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#2: Protein/peptide Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein/peptide Histone H2A /


Mass: 14109.436 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein/peptide Histone H2B 1.1 / H2B1.1


Mass: 13629.911 Da / Num. of mol.: 2 / Mutation: S29T, K117C / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein/peptide Ubiquitin /


Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C / Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62979
#8: Protein/peptide Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone methyltransferase / DOT1-like protein / Histone H3-K79 methyltransferase / H3-K79-HMTase / Lysine N-methyltransferase 4


Mass: 47506.156 Da / Num. of mol.: 1 / Details: S-ADENOSYL-L-HOMOCYSTEINE / Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L, KIAA1814, KMT4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TEK3, histone-lysine N-methyltransferase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (144-MER)


Mass: 45138.770 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (145-MER)


Mass: 45610.043 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 1 molecules

#9: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Formula: C14H20N6O5S / S-Adenosyl-L-homocysteine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Human DOT1L in complex with an H2B-monoubiquitinated nucleosomeCOMPLEX1,2,3,4,5,6,7,80MULTIPLE SOURCES
2Human DOT1L in complex with an H2B-monoubiquitinated nucleosomeCOMPLEX1,2,3,42MULTIPLE SOURCES
3Human DOT1L in complex with an H2B-monoubiquitinated nucleosomeCOMPLEX7,83MULTIPLE SOURCES
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
118355African clawed frog (African clawed frog)
229606Human (human)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 0.98 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software

Classification: refinement / Contact author: Paul D. Adams / Contact author email: pdadams[at]lbl.gov / Language: Python/C++ / Location: https://www.phenix-online.org/ / Type: program / Version: 1.13_2998

Name
phenix.real_space_refine
PHENIX
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 151545 / Symmetry type: POINT
RefineStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007816146
ELECTRON MICROSCOPYf_angle_d0.959823055
ELECTRON MICROSCOPYf_chiral_restr0.05152607
ELECTRON MICROSCOPYf_plane_restr0.00681920
ELECTRON MICROSCOPYf_dihedral_angle_d22.69578736

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