+Open data
-Basic information
Entry | Database: PDB / ID: 4hsu | ||||||
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Title | Crystal structure of LSD2-NPAC with H3(1-26)in space group P21 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / histone demethylase | ||||||
Function / homology | Function and homology information epigenetic programing of female pronucleus / chromatin-protein adaptor activity / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / transcription elongation-coupled chromatin remodeling / histone demethylase activity / nucleosome binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling ...epigenetic programing of female pronucleus / chromatin-protein adaptor activity / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / transcription elongation-coupled chromatin remodeling / histone demethylase activity / nucleosome binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / methylated histone binding / FAD binding / HDMs demethylate histones / structural constituent of chromatin / UCH proteinases / NAD binding / nucleosome / NADP binding / flavin adenine dinucleotide binding / histone binding / oxidoreductase activity / protein heterodimerization activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 Å | ||||||
Authors | Chen, F. / Dong, Z. / Fang, J. / Xu, Y. | ||||||
Citation | Journal: Cell Res. / Year: 2013 Title: Structural insight into substrate recognition by histone demethylase LSD2/KDM1b. Authors: Chen, F. / Yang, H. / Dong, Z. / Fang, J. / Wang, P. / Zhu, T. / Gong, W. / Fang, R. / Shi, Y.G. / Li, Z. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hsu.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hsu.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hsu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hsu_validation.pdf.gz | 754.6 KB | Display | wwPDB validaton report |
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Full document | 4hsu_full_validation.pdf.gz | 771.5 KB | Display | |
Data in XML | 4hsu_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 4hsu_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/4hsu ftp://data.pdbj.org/pub/pdb/validation_reports/hs/4hsu | HTTPS FTP |
-Related structure data
Related structure data | 4gu0C 4gu1S S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 87051.547 Da / Num. of mol.: 1 / Fragment: UNP residues 51-822 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LSD2 / Plasmid: modified pFastBac1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NB78, Oxidoreductases |
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#2: Protein | Mass: 13528.271 Da / Num. of mol.: 1 / Fragment: UNP residues 152-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLYR1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q49A26, Oxidoreductases |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 3177.750 Da / Num. of mol.: 1 / Fragment: UNP residues 2-31 / Mutation: K4M / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133 |
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-Non-polymers , 3 types, 318 molecules
#4: Chemical | ChemComp-FAD / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.988→50 Å / Num. obs: 64821 / % possible obs: 98.99 % / Biso Wilson estimate: 29.89 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GU1 Resolution: 1.988→40.436 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7926 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 27.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.59 Å2 / Biso mean: 38.2711 Å2 / Biso min: 19.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.988→40.436 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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