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- PDB-5hq2: Structural model of Set8 histone H4 Lys20 methyltransferase bound... -
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Open data
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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 | ||||||||||||
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![]() | Transferase/DNA / chromatin enzyme / chromatin complex / epigenetics / histone methyltransferase / Transferase-DNA complex | ||||||||||||
Function / homology | ![]() response to pheromone / histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / Postmitotic nuclear pore complex (NPC) reformation / polytene chromosome / peptidyl-lysine monomethylation / protein-lysine N-methyltransferase activity ...response to pheromone / histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / Postmitotic nuclear pore complex (NPC) reformation / polytene chromosome / peptidyl-lysine monomethylation / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator / poly(A)+ mRNA export from nucleus / nucleus organization / histone methyltransferase activity / negative regulation of double-strand break repair via homologous recombination / ribosomal subunit export from nucleus / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / guanyl-nucleotide exchange factor activity / 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 / nucleosome assembly / 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 | ![]() synthetic construct (others) ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Tavarekere, G. / McGinty, R.K. / Tan, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.8 KB | Display | ![]() |
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PDB format | ![]() | 168.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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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 |
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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.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
#3: Protein | Mass: 13978.241 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 13524.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#7: Protein | Mass: 53095.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SRM1, MTR1, PRP20, YGL097W / Plasmid: pST50Tr / Production host: ![]() ![]() |
#8: Protein | Mass: 23016.270 Da / Num. of mol.: 1 / Mutation: H347F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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: ![]() ![]() |
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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: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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Refine LS restraints |
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