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- PDB-6jm9: cryo-EM structure of DOT1L bound to unmodified nucleosome -

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Entry
Database: PDB / ID: 6jm9
Titlecryo-EM structure of DOT1L bound to unmodified nucleosome
Components
  • DNA strand IDNA
  • DNA strand J
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
KeywordsGENE REGULATION / histone / nucleosome / methylation
Function / homology
Function and homology information


PKMTs methylate histone lysines / histone methyltransferase activity (H3-K79 specific) / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / histone methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / chromatin silencing at telomere / histone-lysine N-methyltransferase / histone-lysine N-methyltransferase activity / telomere organization ...PKMTs methylate histone lysines / histone methyltransferase activity (H3-K79 specific) / regulation of transcription regulatory region DNA binding / histone H3-K79 methylation / histone methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / chromatin silencing at telomere / histone-lysine N-methyltransferase / histone-lysine N-methyltransferase activity / telomere organization / DNA-templated transcription, initiation / DNA damage checkpoint / nucleosome / chromosome, telomeric region / nucleosome assembly / intracellular membrane-bounded organelle / oxidoreductase activity / transcription factor binding / positive regulation of cell population proliferation / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus
Histone-fold / TATA box binding protein associated factor (TAF) / Histone H2A, C-terminal domain / Histone H3-K79 methyltransferase / Histone H2B / Histone H4 / Histone H2A / Alcohol dehydrogenase, zinc-type, conserved site / Histone H2A/H2B/H3 / Histone-lysine N-methyltransferase DOT1 domain ...Histone-fold / TATA box binding protein associated factor (TAF) / Histone H2A, C-terminal domain / Histone H3-K79 methyltransferase / Histone H2B / Histone H4 / Histone H2A / Alcohol dehydrogenase, zinc-type, conserved site / Histone H2A/H2B/H3 / Histone-lysine N-methyltransferase DOT1 domain / S-adenosyl-L-methionine-dependent methyltransferase / GroES-like superfamily / Alcohol dehydrogenase, C-terminal / Alcohol dehydrogenase, N-terminal / Histone H4, conserved site / Polyketide synthase, enoylreductase domain / Histone H2A conserved site / Histone H3-K79 methyltransferase, metazoa / Centromere kinetochore component CENP-T histone fold / Histone H2B signature. / NAD(P)-binding domain superfamily / Zinc-binding dehydrogenase / Core histone H2A/H2B/H3/H4 / Histone methylation protein DOT1 / Alcohol dehydrogenase GroES-like domain / CENP-T/Histone H4, histone fold / C-terminus of histone H2A / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / Histone H2A signature. / Histone H4 signature. / Zinc-containing alcohol dehydrogenases signature.
Histone H2B 1.1 / Histone H4 / Nerol dehydrogenase / Histone H2A / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Specimen sourcesynthetic construct (others)
Xenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsJang, S. / Song, J.J.
Funding supportKorea, Republic Of , 3件
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016R1A2B3006293Korea, Republic Of
National Research Foundation (Korea)NRF-2016K1A1A2912057Korea, Republic Of
National Research Foundation (Korea)NRF- 2016H1A2A1908806Korea, 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 Report
SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2019 / Release: May 15, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 15, 2019Structure modelrepositoryInitial release
1.1May 22, 2019Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
I: DNA strand I
J: DNA strand J
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
X: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,59312
Polymers201,19411
Non-polymers3981
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54520 Å2
ΔGint-361 kcal/mol
Surface area81260 Å2

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Components

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DNA chain , 2 types, 2 molecules IJ

#1: DNA chain DNA strand I / DNA


Mass: 37890.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): DH5[alpha]
#2: DNA chain DNA strand J


Mass: 38010.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): DH5[alpha]

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Protein/peptide , 5 types, 9 molecules AEBFCGDHX

#3: Protein/peptide Histone H3.2


Mass: 11488.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P84233
#4: Protein/peptide Histone H4 /


Mass: 9990.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62799
#5: Protein/peptide Histone H2A /


Mass: 11724.677 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6AZJ8
#6: Protein/peptide Histone H2B 1.1 / H2B1.1


Mass: 10478.032 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02281
#7: Protein/peptide Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone methyltransferase / DOT1-like protein


Mass: 37930.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8TEK3, histone-lysine N-methyltransferase

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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / S-Adenosyl methionine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DOT1L bound to unmodified nucleosome / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.27 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 37.28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21229 / Symmetry type: POINT

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