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Yorodumi- PDB-6kxv: Crystal structure of a nucleosome containing Leishmania histone H3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kxv | ||||||||||||
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Title | Crystal structure of a nucleosome containing Leishmania histone H3 | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Chromatin / Nucleosome / Leishmania / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / 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 ...protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / arachidonate metabolic process / 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 / 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 / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / 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 / 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 / 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 / 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 / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Leishmania major (eukaryote) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.63 Å | ||||||||||||
Authors | Dacher, M. / Taguchi, H. / Kujirai, T. / Kurumizaka, H. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Incorporation and influence of Leishmania histone H3 in chromatin. Authors: Dacher, M. / Tachiwana, H. / Horikoshi, N. / Kujirai, T. / Taguchi, H. / Kimura, H. / Kurumizaka, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kxv.cif.gz | 318.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kxv.ent.gz | 241.4 KB | Display | PDB format |
PDBx/mmJSON format | 6kxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kxv_validation.pdf.gz | 498.2 KB | Display | wwPDB validaton report |
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Full document | 6kxv_full_validation.pdf.gz | 516.6 KB | Display | |
Data in XML | 6kxv_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 6kxv_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/6kxv ftp://data.pdbj.org/pub/pdb/validation_reports/kx/6kxv | HTTPS FTP |
-Related structure data
Related structure data | 5ay8S 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:
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