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Yorodumi- PDB-6le9: The Human Telomeric Nucleosome Displays Distinct Structural and D... -
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-Basic information
Entry | Database: PDB / ID: 6le9 | ||||||
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Title | The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Telomeric DNA / Nucleosome Core Particle / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization ...protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / antibacterial humoral response / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Soman, A. / Liew, C.W. / Teo, H.L. / Berezhnoy, N. / Korolev, N. / Rhodes, D. / Nordenskiold, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: The human telomeric nucleosome displays distinct structural and dynamic properties. Authors: Soman, A. / Liew, C.W. / Teo, H.L. / Berezhnoy, N.V. / Olieric, V. / Korolev, N. / Rhodes, D. / Nordenskiold, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6le9.cif.gz | 309.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6le9.ent.gz | 235.4 KB | Display | PDB format |
PDBx/mmJSON format | 6le9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6le9_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6le9_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6le9_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 6le9_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/6le9 ftp://data.pdbj.org/pub/pdb/validation_reports/le/6le9 | HTTPS FTP |
-Related structure data
Related structure data | 6ke9C 6l9hC 3lz0S 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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1 |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 11269.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68431 #2: Protein | Mass: 9990.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805 #3: Protein | Mass: 11508.419 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04908 #4: Protein | Mass: 10607.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O60814 |
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-Human Telomeric DNA (145- ... , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 43478.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#6: DNA chain | Mass: 46024.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 1 types, 4 molecules
#7: Chemical | ChemComp-MN / |
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-Details
Has ligand of interest | Y |
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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: 2.92 Å3/Da / Density % sol: 57.85 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.518→92.961 Å / Num. obs: 33289 / % possible obs: 94.5 % / Redundancy: 13 % / Biso Wilson estimate: 70.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Rrim(I) all: 0.119 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.518→2.899 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.506 / Num. unique obs: 1665 / CC1/2: 0.795 / Rpim(I) all: 0.426 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LZ0 Resolution: 2.6→49 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.539
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Displacement parameters | Biso max: 200.63 Å2 / Biso mean: 100.24 Å2 / Biso min: 8.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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