+Open data
-Basic information
Entry | Database: PDB / ID: 5b1l | |||||||||
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Title | The mouse nucleosome structure containing H3t | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / chromatin / spermatogenesis / histone-fold / 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 / B-WICH complex positively regulates rRNA expression / chromatin organization => GO:0006325 / Inhibition of DNA recombination at telomere / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...: / : / 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 / B-WICH complex positively regulates rRNA expression / chromatin organization => GO:0006325 / Inhibition of DNA recombination at telomere / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Deposition of new CENPA-containing nucleosomes at the centromere / Chromatin modifying enzymes / 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 / Interleukin-7 signaling / HDMs demethylate histones / Cleavage of the damaged purine / Senescence-Associated Secretory Phenotype (SASP) / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes / Metalloprotease DUBs / HDACs deacetylate histones / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / UCH proteinases / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Factors involved in megakaryocyte development and platelet production / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / heterochromatin organization / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Urahama, T. / Machida, S. / Horikoshi, N. / Osakabe, A. / Tachiwana, H. / Taguchi, H. / Kurumizaka, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Cell Rep / Year: 2017 Title: Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis Authors: Ueda, J. / Harada, A. / Urahama, T. / Machida, S. / Maehara, K. / Hada, M. / Makino, Y. / Nogami, J. / Horikoshi, N. / Osakabe, A. / Taguchi, H. / Tanaka, H. / Tachiwana, H. / Yao, T. / ...Authors: Ueda, J. / Harada, A. / Urahama, T. / Machida, S. / Maehara, K. / Hada, M. / Makino, Y. / Nogami, J. / Horikoshi, N. / Osakabe, A. / Taguchi, H. / Tanaka, H. / Tachiwana, H. / Yao, T. / Yamada, M. / Iwamoto, T. / Isotani, A. / Ikawa, M. / Tachibana, T. / Okada, Y. / Kimura, H. / Ohkawa, Y. / Kurumizaka, H. / Yamagata, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b1l.cif.gz | 329.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b1l.ent.gz | 247.8 KB | Display | PDB format |
PDBx/mmJSON format | 5b1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b1l_validation.pdf.gz | 501.7 KB | Display | wwPDB validaton report |
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Full document | 5b1l_full_validation.pdf.gz | 515.5 KB | Display | |
Data in XML | 5b1l_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 5b1l_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/5b1l ftp://data.pdbj.org/pub/pdb/validation_reports/b1/5b1l | HTTPS FTP |
-Related structure data
Related structure data | 5b1mC 2cv5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15744.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gm12260 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68433*PLUS #2: Protein | Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Gene: Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4 Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62806 #3: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Gene: Hist1h2ab, Hist1h2ac, Hist1h2ad, Hist1h2ae, Hist1h2ag, Hist1h2ai, Hist1h2an, Hist1h2ao Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22752, UniProt: C0HKE1*PLUS #4: Protein | Mass: 14307.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist3h2ba / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9D2U9 |
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-DNA chain , 1 types, 2 molecules IJ
#5: DNA chain | Mass: 45053.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEM-T Easy / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): DH5[alpha] |
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-Non-polymers , 3 types, 242 molecules
#6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-MN / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF HISTONE H3T HAS BEEN REGISTERED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: potassium cacodylate, potassium chloride, manganese chloride |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 3, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→50 Å / Num. obs: 75240 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 40.94 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Χ2: 0.807 / Net I/av σ(I): 20.842 / Net I/σ(I): 5.9 / Num. measured all: 496153 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CV5 Resolution: 2.35→41.833 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.6 / 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: 120.87 Å2 / Biso mean: 48.1914 Å2 / Biso min: 14.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→41.833 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %
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