[English] 日本語
Yorodumi- PDB-1f66: 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f66 | ||||||
---|---|---|---|---|---|---|---|
Title | 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z | ||||||
Components |
| ||||||
Keywords | STRUCTURAL PROTEIN/DNA / NUCLEOSOME / CHROMATIN / HISTONE / HISTONE VARIANT / PROTEIN DNA INTERACTION / NUCLEOPROTEIN / SUPERCOILED DNA / COMPLEX (NUCLEOSOME CORE-DNA) / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / heterochromatin formation => GO:0031507 / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / Recognition and association of DNA glycosylase with site containing an affected purine / HDMs demethylate histones / Cleavage of the damaged purine / Nonhomologous End-Joining (NHEJ) ...Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / heterochromatin formation => GO:0031507 / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / Recognition and association of DNA glycosylase with site containing an affected purine / HDMs demethylate histones / Cleavage of the damaged purine / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / HATs acetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / RNA polymerase II core promoter sequence-specific DNA binding / Packaging Of Telomere Ends / heterochromatin / 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 / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / cellular response to estradiol stimulus / RNA Polymerase I Promoter Opening / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / euchromatin / heterochromatin formation / chromatin DNA binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Suto, R.K. / Clarkson, M.J. / Tremethick, D.J. / Luger, K. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Authors: Suto, R.K. / Clarkson, M.J. / Tremethick, D.J. / Luger, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1f66.cif.gz | 334.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1f66.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 1f66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f66_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1f66_full_validation.pdf.gz | 470 KB | Display | |
Data in XML | 1f66_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 1f66_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/1f66 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/1f66 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
-DNA chain , 1 types, 2 molecules IJ
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically |
---|
-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15507.190 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZT64, UniProt: P84233*PLUS #3: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P62806 #4: Protein | Mass: 13581.796 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PUC / Production host: Escherichia coli (E. coli) / References: UniProt: P17317, UniProt: P0C0S5*PLUS #5: Protein | Mass: 13979.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
---|
-Non-polymers , 2 types, 340 molecules
#6: Chemical | ChemComp-MN / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: used macroseeding | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||
Detector |
| ||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||
Reflection | Resolution: 2.6→25 Å / Num. all: 66416 / Num. obs: 65959 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.7 | ||||||||||||||||||||
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.245 / Num. unique all: 3292 / % possible all: 99.9 | ||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.6→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 25 Å / % reflection Rfree: 3.1 % / Rfactor obs: 0.193 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|