[English] 日本語
Yorodumi- EMDB-0654: Structural basis of Dot1L stimulation by histone H2B lysine 120 u... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0654 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structural basis of Dot1L stimulation by histone H2B lysine 120 ubiquitination. 5.2A reconstruction of Dot1L on H2BK120Ub nucleosome | |||||||||
Map data | Result of cisTEM refinement, filtered to 5.2A, not sharpened. This map is in the same environment as the model constructed. It is shifted and resampled to fit with the environment of the paper | |||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||
Authors | Valencia-Sanchez MI / De Ioannes P / Wang M / Vasilyev N / Chen R / Nudler E / Armache J-P / Armache K-J | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Mol Cell / Year: 2019 Title: Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination. Authors: Marco Igor Valencia-Sánchez / Pablo De Ioannes / Miao Wang / Nikita Vasilyev / Ruoyu Chen / Evgeny Nudler / Jean-Paul Armache / Karim-Jean Armache / Abstract: The essential histone H3 lysine 79 methyltransferase Dot1L regulates transcription and genomic stability and is deregulated in leukemia. The activity of Dot1L is stimulated by mono-ubiquitination of ...The essential histone H3 lysine 79 methyltransferase Dot1L regulates transcription and genomic stability and is deregulated in leukemia. The activity of Dot1L is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120Ub); however, the detailed mechanism is not understood. We report cryo-EM structures of human Dot1L bound to (1) H2BK120Ub and (2) unmodified nucleosome substrates at 3.5 Å and 4.9 Å, respectively. Comparison of both structures, complemented with biochemical experiments, provides critical insights into the mechanism of Dot1L stimulation by H2BK120Ub. Both structures show Dot1L binding to the same extended surface of the histone octamer. In yeast, this surface is used by silencing proteins involved in heterochromatin formation, explaining the mechanism of their competition with Dot1. These results provide a strong foundation for understanding conserved crosstalk between histone modifications found at actively transcribed genes and offer a general model of how ubiquitin might regulate the activity of chromatin enzymes. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0654.map.gz | 44.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0654-v30.xml emd-0654.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_0654.png | 70.6 KB | ||
Others | emd_0654_additional.map.gz emd_0654_half_map_1.map.gz emd_0654_half_map_2.map.gz | 59.3 MB 4.3 MB 4.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0654 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0654 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_0654.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Result of cisTEM refinement, filtered to 5.2A, not sharpened. This map is in the same environment as the model constructed. It is shifted and resampled to fit with the environment of the paper | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Result of cisTEM refinement, filtered to 5.2A, not...
File | emd_0654_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Result of cisTEM refinement, filtered to 5.2A, not sharpened. This map is not in the same environment as the model | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half-map 1
File | emd_0654_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half-map 2
File | emd_0654_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Cryo-EM structure of human Dot1L bound to H2BK120Ub nucleosome at...
Entire | Name: Cryo-EM structure of human Dot1L bound to H2BK120Ub nucleosome at 5.2A resolution |
---|---|
Components |
|
-Supramolecule #1: Cryo-EM structure of human Dot1L bound to H2BK120Ub nucleosome at...
Supramolecule | Name: Cryo-EM structure of human Dot1L bound to H2BK120Ub nucleosome at 5.2A resolution type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK I Details: 3 ul of Dot1L-nucleosome complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 200 mesh), blotted in a Vitrobot Mark III (FEI Company) using 1.5 seconds ...Details: 3 ul of Dot1L-nucleosome complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 200 mesh), blotted in a Vitrobot Mark III (FEI Company) using 1.5 seconds blotting at 100% humidity, and then plunge-frozen in liquid ethane cooled by liquid nitrogen.. |
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Sampling interval: 5.0 µm / Average electron dose: 41.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1607487 |
---|---|
CTF correction | Software - Name: Gctf |
Startup model | Type of model: INSILICO MODEL / In silico model: Generated using cryosparc ab initio run |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85029 |
Details | Frames were motion corrected using MotionCor2 with dose-weighting |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|