+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9784 | |||||||||
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Title | Cryo-EM structure of human DOT1L in complex with nucleosome | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||
Authors | Yao T / Huang J | |||||||||
Funding support | China, 2 items
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Citation | Journal: 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 / | |||||||||
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_9784.map.gz | 28.3 MB | EMDB map data format | |
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Header (meta data) | emd-9784-v30.xml emd-9784.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_9784.png | 455.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9784 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9784 | HTTPS FTP |
-Validation report
Summary document | emd_9784_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_9784_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_9784_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9784 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9784 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9784.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human DOT1L in complex with nucleosome
Entire | Name: human DOT1L in complex with nucleosome |
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Components |
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-Supramolecule #1: human DOT1L in complex with nucleosome
Supramolecule | Name: human DOT1L in complex with nucleosome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 240 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.98 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: an initial model generated from a subset of the dataset |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131329 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |