+Open data
-Basic information
Entry | Database: PDB / ID: 3zmu | ||||||
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Title | LSD1-CoREST in complex with PKSFLV peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / CHROMATIN | ||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / regulation of androgen receptor signaling pathway / MRF binding / 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 / positive regulation of epithelial to mesenchymal transition / cellular response to cAMP / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Regulation of PTEN gene transcription / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / positive regulation of protein ubiquitination / negative regulation of protein binding / HDACs deacetylate histones / promoter-specific chromatin binding / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of DNA-binding transcription factor activity / p53 binding / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / regulation of protein localization / cellular response to UV / Factors involved in megakaryocyte development and platelet production / chromatin organization / positive regulation of cold-induced thermogenesis / flavin adenine dinucleotide binding / chromosome, telomeric region / DNA-binding transcription factor binding / Potential therapeutics for SARS / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / oxidoreductase activity / chromatin remodeling / 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 / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Tortorici, M. / Borrello, M.T. / Tardugno, M. / Chiarelli, L.R. / Pilotto, S. / Ciossani, G. / Vellore, N.A. / Cowan, J. / O'Connell, M. / Mai, A. ...Tortorici, M. / Borrello, M.T. / Tardugno, M. / Chiarelli, L.R. / Pilotto, S. / Ciossani, G. / Vellore, N.A. / Cowan, J. / O'Connell, M. / Mai, A. / Baron, R. / Ganesan, A. / Mattevi, A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Protein Recognition by Small Peptide Reversible Inhibitors of the Chromatin-Modifying Lsd1/Corest Lysine Demethylase. Authors: Tortorici, M. / Borrello, M.T. / Tardugno, M. / Chiarelli, L.R. / Pilotto, S. / Ciossani, G. / Vellore, N.A. / Bailey, S.G. / Cowan, J. / O'Connell, M. / Crabb, S.J. / Packham, G.K. / Mai, A. ...Authors: Tortorici, M. / Borrello, M.T. / Tardugno, M. / Chiarelli, L.R. / Pilotto, S. / Ciossani, G. / Vellore, N.A. / Bailey, S.G. / Cowan, J. / O'Connell, M. / Crabb, S.J. / Packham, G.K. / Mai, A. / Baron, R. / Ganesan, A. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zmu.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zmu.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 3zmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zmu_validation.pdf.gz | 740.3 KB | Display | wwPDB validaton report |
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Full document | 3zmu_full_validation.pdf.gz | 745.2 KB | Display | |
Data in XML | 3zmu_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3zmu_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/3zmu ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zmu | HTTPS FTP |
-Related structure data
Related structure data | 3zmsC 3zmtC 3zmvC 3zmzC 3zn0C 3zn1C 2y48S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 94820.195 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) / Strain (production host): BL21 / References: UniProt: O60341, Oxidoreductases |
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#2: Protein | Mass: 53101.961 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) / Strain (production host): BL21 / References: UniProt: Q9UKL0 |
#3: Protein/peptide | Mass: 690.850 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) / Strain (production host): BL21 |
#4: Chemical | ChemComp-FAD / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.26 Å3/Da / Density % sol: 75 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→72 Å / Num. obs: 42014 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y48 Resolution: 3.2→62.75 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.677 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.566 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→62.75 Å
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Refine LS restraints |
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