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Yorodumi- PDB-6vyp: Crystal structure of the LSD1/CoREST histone demethylase bound to... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 6vyp | ||||||||||||
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| Title | Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate | ||||||||||||
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Keywords | NUCLEAR PROTEIN/DNA / epigenetics / histone modifications / histone demethylation / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex | ||||||||||||
| Function / homology | Function and homology informationpositive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development / positive regulation of neural precursor cell proliferation / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / nuclear androgen receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / histone H3K9 demethylase activity / histone deacetylase complex / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase complex / histone demethylase activity / positive regulation of cell size / positive regulation of epithelial to mesenchymal transition / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / epigenetic regulation of gene expression / cellular response to cAMP / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / erythrocyte differentiation / HDACs deacetylate histones / promoter-specific chromatin binding / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / positive regulation of neuron projection development / cerebral cortex development / protein modification process / p53 binding / cellular response to UV / structural constituent of chromatin / transcription corepressor activity / heterochromatin formation / nucleosome / flavin adenine dinucleotide binding / nucleosome assembly / regulation of protein localization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / chromatin organization / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor binding / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / oxidoreductase activity / chromosome, telomeric region / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||||||||
| Biological species | synthetic construct (others) Homo sapiens (human) | ||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.99 Å | ||||||||||||
Authors | Kim, S. / Zhu, J. / Eek, P. / Yennawar, N. / Song, T. | ||||||||||||
| Funding support | United States, 3items
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Citation | Journal: Mol.Cell / Year: 2020Title: Crystal Structure of the LSD1/CoREST Histone Demethylase Bound to Its Nucleosome Substrate. Authors: Kim, S.A. / Zhu, J. / Yennawar, N. / Eek, P. / Tan, S. | ||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6vyp.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb6vyp.ent.gz | 2.3 MB | Display | PDB format |
| PDBx/mmJSON format | 6vyp.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6vyp_validation.pdf.gz | 536.4 KB | Display | wwPDB validaton report |
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| Full document | 6vyp_full_validation.pdf.gz | 541 KB | Display | |
| Data in XML | 6vyp_validation.xml.gz | 2.9 KB | Display | |
| Data in CIF | 6vyp_validation.cif.gz | 52.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/6vyp ftp://data.pdbj.org/pub/pdb/validation_reports/vy/6vyp | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 3lz0S S: Starting model for refinement |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
United States, 3items
Citation






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