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Yorodumi- PDB-1kna: Chromo domain of HP1 complexed with histone H3 tail containing di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kna | ||||||
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Title | Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9. | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / chromo / HP1 / histone / dimethyllysine / methyllysine / H3 | ||||||
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 / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression ...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 / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / RNA polymerase II C-terminal domain binding / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / satellite DNA binding / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / positive regulation of DNA methylation-dependent heterochromatin formation / polytene chromosome / chromocenter / rDNA binding / pericentric heterochromatin formation / condensed chromosome, centromeric region / regulation of protein localization to chromatin / RNA polymerase binding / condensed chromosome / chromosome, centromeric region / chromosome organization / heterochromatin / pericentric heterochromatin / nucleosomal DNA binding / Hsp70 protein binding / methylated histone binding / telomere maintenance / euchromatin / heterochromatin formation / structural constituent of chromatin / chromosome / nucleosome / nucleosome assembly / mitotic cell cycle / protein-macromolecule adaptor activity / histone binding / chromosome, telomeric region / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / mRNA binding / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / protein-containing complex binding / 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: 2.1 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 | 1kna.cif.gz | 23.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kna.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kna_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 1kna_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 1kna_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1kna_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1kna ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1kna | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 8586.468 Da / Num. of mol.: 1 / Fragment: Residues 23-76 / 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: 1756.017 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 dimethylated. 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: 2.37 Å3/Da / Density % sol: 48.14 % | |||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Ammonium Sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283.0K | |||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / pH: 6.1 / 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 10, 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: 2.1→30 Å / Num. all: 6032 / Num. obs: 6032 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 61.6 |
Reflection shell | Resolution: 2.1→2.23 Å / Mean I/σ(I) obs: 10.5 / Num. unique all: 842 / Rsym value: 0.279 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 2.1 Å / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.279 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.63 Å / Rfactor Rfree error: 0.026 / Data cutoff high rms absF: 117307.12 / 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: 2.1→28.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor obs: 0.228 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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