+Open data
-Basic information
Entry | Database: PDB / ID: 6jm9 | ||||||||||||
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Title | cryo-EM structure of DOT1L bound to unmodified nucleosome | ||||||||||||
Components |
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Keywords | GENE REGULATION / histone / nucleosome / methylation | ||||||||||||
Function / homology | Function and homology information histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / telomere organization / DNA damage checkpoint signaling / PKMTs methylate histone lysines ...histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / telomere organization / DNA damage checkpoint signaling / PKMTs methylate histone lysines / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / gene expression / methylation / transcription coactivator activity / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein heterodimerization activity / intracellular membrane-bounded organelle / DNA repair / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | synthetic construct (others) Xenopus laevis (African clawed frog) Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.3 Å | ||||||||||||
Authors | Jang, S. / Song, J.J. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: 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. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jm9.cif.gz | 354.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jm9.ent.gz | 269.6 KB | Display | PDB format |
PDBx/mmJSON format | 6jm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jm9_validation.pdf.gz | 992.2 KB | Display | wwPDB validaton report |
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Full document | 6jm9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6jm9_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 6jm9_validation.cif.gz | 71.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/6jm9 ftp://data.pdbj.org/pub/pdb/validation_reports/jm/6jm9 | HTTPS FTP |
-Related structure data
Related structure data | 9843MC 9844C 6jmaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA chain , 2 types, 2 molecules IJ
#1: DNA chain | 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] |
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#2: DNA chain | 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] |
-Protein , 5 types, 9 molecules AEBFCGDHX
#3: Protein | 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 | 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 | 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 | 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 | | 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 / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DOT1L bound to unmodified nucleosome / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.27 MDa / Experimental value: NO |
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) / Strain: BL21 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 37.28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21229 / Symmetry type: POINT |