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- PDB-3x1t: Crystal structure of nucleosome core particle consisting of mouse... -
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Basic information
Entry | Database: PDB / ID: 3x1t | ||||||
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Title | Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba | ||||||
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![]() | STRUCTURAL PROTEIN/DNA / Histone variants of h2a and h2b / reprogramming / chromatin / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | ![]() Deposition of new CENPA-containing nucleosomes at the centromere / E3 ubiquitin ligases ubiquitinate target proteins / G2/M DNA damage checkpoint / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes / Metalloprotease DUBs / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / UCH proteinases / HATs acetylate histones ...Deposition of new CENPA-containing nucleosomes at the centromere / E3 ubiquitin ligases ubiquitinate target proteins / G2/M DNA damage checkpoint / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes / Metalloprotease DUBs / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / UCH proteinases / HATs acetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / sperm DNA condensation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / mononuclear cell migration / nucleosome disassembly / Ub-specific processing proteases / female germ cell nucleus / plasminogen activation / chromosome organization / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / 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 / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / 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 / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cadherin binding / inflammatory response / protein heterodimerization activity / Amyloid fiber formation / cell surface / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() synthetic (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sivaraman, P. / Kumarevel, T.S. | ||||||
![]() | ![]() Title: Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming Authors: Padavattan, S. / Shinagawa, T. / Hasegawa, K. / Kumasaka, T. / Ishii, S. / Kumarevel, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.9 KB | Display | ![]() |
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PDB format | ![]() | 248.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.3 KB | Display | ![]() |
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Full document | ![]() | 513.6 KB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 51.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3x1sC ![]() 3x1uC ![]() 3x1vC ![]() 1aoiS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic (others) |
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-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15305.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13952.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Protein | Mass: 14136.502 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 3 types, 143 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 60-70mM Kcl, 70-90mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2012 |
Radiation | Monochromator: S II / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. all: 51865 / Num. obs: 51865 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.128 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.72 / Num. unique all: 5066 / % possible all: 99.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1AOI Resolution: 2.808→34.96 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 26.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.69 Å2 / Biso mean: 73.1979 Å2 / Biso min: 14.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.808→34.96 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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