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Yorodumi- PDB-6vyp: Crystal structure of the LSD1/CoREST histone demethylase bound to... -
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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 | ||||||||||||
Components |
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Keywords | NUCLEAR PROTEIN/DNA / epigenetics / histone modifications / histone demethylation / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity ...positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity / positive regulation of neural precursor cell proliferation / neuron maturation / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / promoter-specific chromatin binding / HDACs deacetylate histones / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / cerebral cortex development / structural constituent of chromatin / transcription corepressor activity / cellular response to UV / regulation of protein localization / nucleosome / p53 binding / flavin adenine dinucleotide binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) 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: 2020 Title: 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. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-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
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/6vyp ftp://data.pdbj.org/pub/pdb/validation_reports/vy/6vyp | HTTPS FTP |
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-Related structure data
Related structure data | 3lz0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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