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Yorodumi- EMDB-9384: Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9384 | |||||||||
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Title | Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex | |||||||||
Map data | Sharpened map for the structure of Dot1L bound to a ubiquitinated nucleosome | |||||||||
Sample |
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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 / hypothalamus gonadotrophin-releasing hormone neuron development / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule ...histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / hypothalamus gonadotrophin-releasing hormone neuron development / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / histone methyltransferase activity / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / telomere organization / neuron projection morphogenesis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / DNA damage checkpoint signaling / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Worden EJ / Hoffmann NA / Wolberger C | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2019 Title: Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L. Authors: Evan J Worden / Niklas A Hoffmann / Chad W Hicks / Cynthia Wolberger / Abstract: Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is ...Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is conserved from yeast to humans. We report here cryo-EM structures of Dot1L bound to ubiquitinated nucleosome that show how H2B-Ub stimulates Dot1L activity and reveal a role for the histone H4 tail in positioning Dot1L. We find that contacts mediated by Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to insert into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9384.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-9384-v30.xml emd-9384.xml | 36 KB 36 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9384_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_9384.png | 184.4 KB | ||
Masks | emd_9384_msk_1.map | 64 MB | Mask map | |
Others | emd_9384_additional.map.gz emd_9384_additional_1.map.gz emd_9384_half_map_1.map.gz emd_9384_half_map_2.map.gz | 48.2 MB 48.2 MB 59.8 MB 59.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9384 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9384 | HTTPS FTP |
-Validation report
Summary document | emd_9384_validation.pdf.gz | 620.9 KB | Display | EMDB validaton report |
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Full document | emd_9384_full_validation.pdf.gz | 620.5 KB | Display | |
Data in XML | emd_9384_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_9384_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9384 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9384 | HTTPS FTP |
-Related structure data
Related structure data | 6nj9MC 0468C 0480C 6nogC 6nqaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9384.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map for the structure of Dot1L bound to a ubiquitinated nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_9384_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map for the structure of Dot1L bound...
File | emd_9384_additional.map | ||||||||||||
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Annotation | Unsharpened map for the structure of Dot1L bound to a ubiquitinated nucleosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map for the structure of Dot1L bound...
File | emd_9384_additional_1.map | ||||||||||||
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Annotation | Unsharpened map for the structure of Dot1L bound to a ubiquitinated nucleosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Sharpened half map used for structure building and refinement
File | emd_9384_half_map_1.map | ||||||||||||
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Annotation | Sharpened half map used for structure building and refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Sharpened half map used for structure validation
File | emd_9384_half_map_2.map | ||||||||||||
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Annotation | Sharpened half map used for structure validation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Active state Dot1L in complex with the H2B-Ub nucleosome
+Supramolecule #1: Active state Dot1L in complex with the H2B-Ub nucleosome
+Supramolecule #2: Dot1L
+Supramolecule #3: H2H2B-Ub nucleosome
+Supramolecule #4: histone core
+Supramolecule #5: ubiquitin
+Supramolecule #6: DNA
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Histone-lysine N-methyltransferase, H3 lysine-79 specific
+Macromolecule #8: Ubiquitin
+Macromolecule #5: 601 DNA Strand 1
+Macromolecule #6: 601 DNA Strand 2
+Macromolecule #9: S-ADENOSYLMETHIONINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.75 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use. | ||||||||||||
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot once for 3.5 seconds before freezing.. | ||||||||||||
Details | Crosslinked with glutaraldehyde |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 2284 / Average exposure time: 8.2 sec. / Average electron dose: 50.0 e/Å2 / Details: 3 exposures per hole |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: OTHER | ||||||||||||||||||||||||||
Output model | PDB-6nj9: |