+Open data
-Basic information
Entry | Database: PDB / ID: 4gu0 | ||||||
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Title | Crystal structure of LSD2 with H3 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / histone demethylase | ||||||
Function / homology | Function and homology information epigenetic programing of female pronucleus / negative regulation of chromosome condensation / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore ...epigenetic programing of female pronucleus / negative regulation of chromosome condensation / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nucleus organization / spermatid development / histone demethylase activity / subtelomeric heterochromatin formation / Replacement of protamines by nucleosomes in the male pronucleus / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / telomere organization / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / embryo implantation / FAD binding / DNA methylation / transcription initiation-coupled chromatin remodeling / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / structural constituent of chromatin / male gonad development / UCH proteinases / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / flavin adenine dinucleotide binding / histone binding / chromosome, telomeric region / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / oxidoreductase activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / chromatin / protein-containing complex / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.103 Å | ||||||
Authors | Chen, F. / Yang, H. / Dong, Z. / Fang, J. / Zhu, T. / Gong, W. / 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 | 4gu0.cif.gz | 600 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gu0.ent.gz | 488.3 KB | Display | PDB format |
PDBx/mmJSON format | 4gu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gu0_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4gu0_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4gu0_validation.xml.gz | 109.9 KB | Display | |
Data in CIF | 4gu0_validation.cif.gz | 142.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/4gu0 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/4gu0 | HTTPS FTP |
-Related structure data
Related structure data | 4hsuC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 87051.547 Da / Num. of mol.: 4 / Fragment: UNP residues 51-822 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LSD2 / Plasmid: pFastBac1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NB78, Oxidoreductases #2: Protein/peptide | Mass: 2793.299 Da / Num. of mol.: 2 / Fragment: UNP residues 2-27 / Mutation: K4M / Source method: obtained synthetically / Details: H3K4 is mutated to Met / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243 #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-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: Mar 26, 2012 |
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: 3.1→50 Å / Num. all: 71966 / Num. obs: 68642 / % possible obs: 94.23 % / Biso Wilson estimate: 66.84 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GU1 Resolution: 3.103→45.059 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8527 / SU ML: 0.32 / σ(F): 0.11 / Phase error: 22.25 / 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 / Bsol: 26.728 Å2 / ksol: 0.29 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.8 Å2 / Biso mean: 77.403 Å2 / Biso min: 38.26 Å2
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Refinement step | Cycle: LAST / Resolution: 3.103→45.059 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: 25
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