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Yorodumi- PDB-1kne: Chromo domain of HP1 complexed with histone H3 tail containing tr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kne | ||||||
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Title | Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / chromo / HP1 / histone / trimethyllysine / methyllysine / H3 / chromatin | ||||||
Function / homology | Function and homology information protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / satellite DNA binding / positive regulation of DNA methylation-dependent heterochromatin formation / pericentric heterochromatin formation / chromocenter / polytene chromosome / rDNA binding / condensed chromosome, centromeric region / regulation of protein localization to chromatin / RNA polymerase binding / nucleosomal DNA binding / RNA polymerase II C-terminal domain binding / chromosome, centromeric region / chromosome organization / heterochromatin / pericentric heterochromatin / heterochromatin formation / condensed chromosome / Hsp70 protein binding / methylated histone binding / telomere maintenance / euchromatin / nucleosome assembly / structural constituent of chromatin / nucleosome / protein-macromolecule adaptor activity / mitotic cell cycle / chromosome / chromatin organization / histone binding / chromosome, telomeric region / protein heterodimerization activity / negative regulation of gene expression / mRNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Jacobs, S.A. / Khorasanizadeh, S. | ||||||
Citation | Journal: Science / Year: 2002 Title: Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Authors: Jacobs, S.A. / Khorasanizadeh, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kne.cif.gz | 23.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kne.ent.gz | 17.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1kne ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1kne | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8586.468 Da / Num. of mol.: 1 / Fragment: Residues 17-76 / Mutation: K38M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3)pLysS / References: UniProt: P05205 |
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#2: Protein/peptide | Mass: 1771.051 Da / Num. of mol.: 1 / Fragment: Residues 1-16 / Mutation: P16Y / Source method: obtained synthetically Details: Synthetic peptide corresponding to residues 1-16 of Histone H3. K9 trimethylated. P16Y mutation References: UniProt: P02299 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % | |||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: Ammonium Sulfate, MES, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K | |||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Oct 30, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 4071 / Num. obs: 4071 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.083 / Net I/σ(I): 47.2 |
Reflection shell | Resolution: 2.4→2.55 Å / Mean I/σ(I) obs: 15.1 / Num. unique all: 631 / Rsym value: 0.297 / % possible all: 95 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 4086 / % possible obs: 99.5 % / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS Lowest resolution: 2.49 Å / % possible obs: 95 % / Rmerge(I) obs: 0.297 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→28.62 Å / Rfactor Rfree error: 0.013 / Data cutoff high rms absF: 102003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→28.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.246 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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