+Open data
-Basic information
Entry | Database: PDB / ID: 6px1 | ||||||
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Title | Set2 bound to nucleosome | ||||||
Components |
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Keywords | GENE REGULATION / Set2 / nucleosome / chromatin / KMT | ||||||
Function / homology | Function and homology information ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / structural constituent of chromatin / protein tag activity / nucleosome / nucleosome assembly / ribosome biogenesis / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit ...ribosomal large subunit export from nucleus / modification-dependent protein catabolic process / structural constituent of chromatin / protein tag activity / nucleosome / nucleosome assembly / ribosome biogenesis / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / protein ubiquitination / structural constituent of ribosome / protein heterodimerization activity / ubiquitin protein ligase binding / mitochondrion / DNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Halic, M. / Bilokapic, S. | ||||||
Citation | Journal: Nat Commun / Year: 2019 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6px1.cif.gz | 287 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6px1.ent.gz | 212.8 KB | Display | PDB format |
PDBx/mmJSON format | 6px1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6px1_validation.pdf.gz | 940.6 KB | Display | wwPDB validaton report |
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Full document | 6px1_full_validation.pdf.gz | 944.4 KB | Display | |
Data in XML | 6px1_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 6px1_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/6px1 ftp://data.pdbj.org/pub/pdb/validation_reports/px/6px1 | HTTPS FTP |
-Related structure data
Related structure data | 20516MC 0559C 6nzoC 6px3C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15437.144 Da / Num. of mol.: 2 / Mutation: K36M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1, UniProt: P02302*PLUS #2: Protein | Mass: 11394.426 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 (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 24045.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Xenopus laevis (African clawed frog) Strain: ATCC 204508 / S288c Gene: RPL40B, UBI2, YKR094C, hist1h2aj, LOC494591, XELAEV_18003602mg Production host: Escherichia coli (E. coli) / References: UniProt: P0CH09, UniProt: Q6AZJ8 #4: Protein | Mass: 13655.948 Da / Num. of mol.: 2 / Mutation: S29T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45764.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 46222.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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 |
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Molecular weight | Value: 0.2 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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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
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 75 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3546: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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