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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20517 | |||||||||
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Title | Set2 bound to nucleosome | |||||||||
![]() | Set2 bound to nucleosome, Class Ub | |||||||||
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Function / homology | ![]() : / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 methyltransferase activity / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / modification-dependent protein catabolic process / structural constituent of chromatin / protein tag activity / nucleosome / nucleosome assembly ...: / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 methyltransferase activity / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / modification-dependent protein catabolic process / structural constituent of chromatin / protein tag activity / nucleosome / nucleosome assembly / ribosome biogenesis / chromosome / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / protein heterodimerization activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Halic M / Bilokapic S | |||||||||
![]() | ![]() Title: Nucleosome and ubiquitin position Set2 to methylate H3K36. Authors: Silvija Bilokapic / Mario Halic / ![]() Abstract: Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes ...Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes cancer progression, however, mechanisms of H3K36me are poorly understood. Set2 enzymes show spurious activity on histones and histone tails, and it is unknown how they obtain specificity to methylate H3K36 on the nucleosome. In this study, we present 3.8 Å cryo-EM structure of Set2 bound to the mimic of H2B ubiquitinated nucleosome. Our structure shows that Set2 makes extensive interactions with the H3 αN, the H3 tail, the H2A C-terminal tail and stabilizes DNA in the unwrapped conformation, which positions Set2 to specifically methylate H3K36. Moreover, we show that ubiquitin contributes to Set2 positioning on the nucleosome and stimulates the methyltransferase activity. Notably, our structure uncovers interfaces that can be targeted by small molecules for development of future cancer therapies. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 47.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.4 KB 20.4 KB | Display Display | ![]() |
Images | ![]() | 424 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 414.4 KB | Display | ![]() |
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Full document | ![]() | 413.9 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6px3MC ![]() 0559C ![]() 6nzoC ![]() 6px1C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Set2 bound to nucleosome, Class Ub | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Set2 bound to ubiquitinated nucleosome
+Supramolecule #1: Set2 bound to ubiquitinated nucleosome
+Supramolecule #2: Histone-lysine N-methyltransferase
+Supramolecule #3: DNA
+Supramolecule #4: Histone H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histo...
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Ubiquitin-60S ribosomal protein L40,Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Histone-lysine N-methyltransferase
+Macromolecule #5: DNA (145-MER)
+Macromolecule #6: DNA (145-MER)
+Macromolecule #8: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Average electron dose: 75.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 BASE (4k x 4k) / #1 - Average electron dose: 75.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K2 BASE (4k x 4k) / #2 - Average electron dose: 75.0 e/Å2 / #3 - Image recording ID: 4 / #3 - Film or detector model: GATAN K2 BASE (4k x 4k) / #3 - Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Image recording ID | 1 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |