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Yorodumi- PDB-5hq2: Structural model of Set8 histone H4 Lys20 methyltransferase bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hq2 | ||||||||||||
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Title | Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle | ||||||||||||
Components |
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Keywords | Transferase/DNA / chromatin enzyme / chromatin complex / epigenetics / histone methyltransferase / Transferase-DNA complex | ||||||||||||
Function / homology | Function and homology information histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / response to pheromone / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / Postmitotic nuclear pore complex (NPC) reformation / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity ...histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / response to pheromone / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / Postmitotic nuclear pore complex (NPC) reformation / peptidyl-lysine monomethylation / polytene chromosome / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / : / poly(A)+ mRNA export from nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / nucleus organization / negative regulation of double-strand break repair via homologous recombination / histone methyltransferase activity / ribosomal subunit export from nucleus / Transferases; Transferring one-carbon groups; Methyltransferases / guanyl-nucleotide exchange factor activity / Condensation of Prophase Chromosomes / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / protein import into nucleus / structural constituent of chromatin / transcription corepressor activity / nucleosome / cell cycle / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) synthetic construct (others) Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | ||||||||||||
Authors | Tavarekere, G. / McGinty, R.K. / Tan, S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate. Authors: Girish, T.S. / McGinty, R.K. / Tan, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hq2.cif.gz | 249.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hq2.ent.gz | 168.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/5hq2 ftp://data.pdbj.org/pub/pdb/validation_reports/hq/5hq2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Gel filtration used to confirm assembly |
-Components
-Protein , 6 types, 6 molecules ABGHKM
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233 |
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#2: Protein | Mass: 11263.231 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799 |
#3: Protein | Mass: 13978.241 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS |
#4: Protein | Mass: 13524.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281 |
#7: Protein | Mass: 53095.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SRM1, MTR1, PRP20, YGL097W / Plasmid: pST50Tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P21827 |
#8: Protein | Mass: 23016.270 Da / Num. of mol.: 1 / Mutation: H347F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD8, KMT5A, PRSET7, SET07, SET8 / Plasmid: pST50Tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS References: UniProt: Q9NQR1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase |
-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45772.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: WIDOM 601 nucleosome positioning sequence / Plasmid: plasmid / Details (production host): PST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 |
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#6: DNA chain | Mass: 46212.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: WIDOM 601 nucleosome positioning sequence / Plasmid: plasmid / Details (production host): PST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.37 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 5.5 Details: 25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME PH range: 5.5-6 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid N2 stream |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→46.19 Å / Num. all: 16854 / Num. obs: 16854 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 4.5→4.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→46 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.832 / SU B: 124.392 / SU ML: 1.58 / Cross valid method: THROUGHOUT / ESU R Free: 1.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 171.987 Å2
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Refinement step | Cycle: LAST / Resolution: 4.5→46 Å
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