+Open data
-Basic information
Entry | Database: PDB / ID: 3zms | ||||||
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Title | LSD1-CoREST in complex with INSM1 peptide | ||||||
Components |
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Keywords | OXIDOREDUCTASE/PEPTIDE / OXIDOREDUCTASE-PEPTIDE COMPLEX / DEMETHYLASE / TRANSCRIPTION FACTOR / CHROMATIN | ||||||
Function / homology | Function and homology information adrenal chromaffin cell differentiation / Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells / pancreatic A cell differentiation / type B pancreatic cell differentiation / noradrenergic neuron development / transdifferentiation / norepinephrine biosynthetic process / regulation of cell cycle process / positive regulation of megakaryocyte differentiation / guanine metabolic process ...adrenal chromaffin cell differentiation / Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells / pancreatic A cell differentiation / type B pancreatic cell differentiation / noradrenergic neuron development / transdifferentiation / norepinephrine biosynthetic process / regulation of cell cycle process / 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 / sympathetic ganglion development / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / type B pancreatic cell development / 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 / regulation of protein-containing complex assembly / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / transcription repressor complex / cyclin binding / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein phosphorylation / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / promoter-specific chromatin binding / HDACs deacetylate histones / positive regulation of cell differentiation / 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 / chromatin DNA binding / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / transcription corepressor activity / cellular response to UV / regulation of protein localization / cell migration / p53 binding / flavin adenine dinucleotide binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / regulation of gene expression / DNA-binding transcription factor binding / Estrogen-dependent gene expression / cell population proliferation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / molecular adaptor activity / regulation of cell cycle / positive regulation of cell migration / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / 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 / nucleoplasm / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 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 | 3zms.cif.gz | 193.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zms.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/3zms ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zms | HTTPS FTP |
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-Related structure data
Related structure data | 3zmtC 3zmuC 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: 94846.234 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 | Mass: 52874.160 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: Q01101 |
#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: 3.14 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: ESRF / Beamline: ID14-1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→75 Å / Num. obs: 52616 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.9 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y48 Resolution: 2.96→63.45 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.023 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.239 / 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: 94.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.96→63.45 Å
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