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Yorodumi- PDB-1kx4: X-Ray Structure of the Nucleosome Core Particle, NCP146b, at 2.6 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kx4 | ||||||
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Title | X-Ray Structure of the Nucleosome Core Particle, NCP146b, at 2.6 A Resolution | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / NUCLEOSOME / CHROMATIN / HISTONE / PROTEIN-DNA INTERACTION / NUCLEOPROTEIN / SUPERCOILED DNA / NUCLEOSOME CORE / PROTEIN-DNA COMPLEX / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information : / : / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / Assembly of the ORC complex at the origin of replication / Transcriptional regulation by small RNAs / chromatin organization => GO:0006325 / B-WICH complex positively regulates rRNA expression / HDACs deacetylate histones / chromatin organization => GO:0006325 ...: / : / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / Assembly of the ORC complex at the origin of replication / Transcriptional regulation by small RNAs / chromatin organization => GO:0006325 / B-WICH complex positively regulates rRNA expression / HDACs deacetylate histones / chromatin organization => GO:0006325 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / Senescence-Associated Secretory Phenotype (SASP) / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / Oxidative Stress Induced Senescence / DNA replication-dependent chromatin assembly / nuclear chromosome / stem cell population maintenance / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / protein domain specific binding / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Davey, C.A. / Sargent, D.F. / Luger, K. / Maeder, A.W. / Richmond, T.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution Authors: Davey, C.A. / Sargent, D.F. / Luger, K. / Maeder, A.W. / Richmond, T.J. #1: Journal: Nature / Year: 1997 Title: Crystal structure of the nucleosome core particle at 2.8 A resolution Authors: Luger, K. / Maeder, A.W. / Richmond, R.K. / Sargent, D.F. / Richmond, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kx4.cif.gz | 326.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kx4.ent.gz | 251.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/1kx4 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/1kx4 | HTTPS FTP |
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-Related structure data
Related structure data | 1kx3C 1kx5C 1aoiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-DNA chain , 1 types, 2 molecules IJ
#1: DNA chain | Mass: 45054.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: palindromic 146 base pair DNA duplex / Source: (gene. exp.) Homo sapiens (human) Description: DNA SEQUENCE SYNTHESIZED, CLONED, MULTIMERIZED, AND EXCISED FROM PLASMID Production host: Escherichia coli (E. coli) |
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-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15303.930 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: P16105, UniProt: P84233*PLUS #3: Protein | Mass: 11263.231 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: P02304, UniProt: P62799*PLUS #4: Protein | Mass: 13907.163 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: P06897 #5: Protein | Mass: 13848.097 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: P02281 |
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-Non-polymers , 3 types, 443 molecules
#6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.85 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 2, 1996 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 67577 / Num. obs: 60481 / % possible obs: 89.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.157 / % possible all: 45.7 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 45.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AOI Resolution: 2.6→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2275168.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 51.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.75 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 6 Å / Rfactor Rfree: 0.3 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.68 Å / Rfactor Rfree: 0.361 / Rfactor Rwork: 0.329 |