[English] 日本語
Yorodumi- PDB-3c1b: The effect of H3 K79 dimethylation and H4 K20 trimethylation on n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c1b | ||||||
---|---|---|---|---|---|---|---|
Title | The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure | ||||||
Components |
| ||||||
Keywords | Structural PROTEIN/DNA / Nucleosome / Dimethylated histone / trimethylated histone / methylation / nucleosomal surface / histone modification / nucleosomal array / chromatin / Acetylation / Chromosomal protein / DNA-binding / Nucleosome core / Nucleus / Phosphoprotein / Ubl conjugation / Structural PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Packaging Of Telomere Ends / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Ub-specific processing proteases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends ...Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Packaging Of Telomere Ends / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Ub-specific processing proteases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Deposition of new CENPA-containing nucleosomes at the centromere / E3 ubiquitin ligases ubiquitinate target proteins / : / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / : / NoRC negatively regulates rRNA expression / : / Transcriptional regulation by small RNAs / : / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) Xenopus tropicalis | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lu, X. / Simon, M. / Chodaparambil, J. / Hansen, J. / Shokat, K. / Luger, K. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Authors: Lu, X. / Simon, M.D. / Chodaparambil, J.V. / Hansen, J.C. / Shokat, K.M. / Luger, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3c1b.cif.gz | 311.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3c1b.ent.gz | 236.3 KB | Display | PDB format |
PDBx/mmJSON format | 3c1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/3c1b ftp://data.pdbj.org/pub/pdb/validation_reports/c1/3c1b | HTTPS FTP |
---|
-Related structure data
Related structure data | 3c1cC 1aoiS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: 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) / Gene: Histone H3 / Production host: Escherichia coli (E. coli) / References: UniProt: P02302, UniProt: P84233*PLUS #2: Protein | Mass: 11323.350 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H4 / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 14008.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H2A / Production host: Escherichia coli (E. coli) / References: UniProt: P06897 #4: Protein | Mass: 13808.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus (Silurana) tropicalis (tropical clawed frog) Gene: hist2h2bf, TGas058p09.1-001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q28D68 |
---|
-DNA chain / Non-polymers , 2 types, 789 molecules IJ
#5: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.4 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Manganese chloride, Potassium chloride, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 292 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 |
Detector | Detector: CCD / Date: Oct 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→43 Å / Num. obs: 106458 / % possible obs: 99 % / Observed criterion σ(F): 4.8 / Observed criterion σ(I): 10.2 / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 99 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1aoi Resolution: 2.2→43 Å / Cross valid method: throught / Stereochemistry target values: Engh & Huber
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43 Å
| ||||||||||||||||
Refine LS restraints |
|