+Open data
-Basic information
Entry | Database: PDB / ID: 4gur | ||||||
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Title | Crystal structure of LSD2-NPAC with H3 in space group P21 | ||||||
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 / chromatin-protein adaptor activity / 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 ...epigenetic programing of female pronucleus / negative regulation of chromosome condensation / chromatin-protein adaptor activity / 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 / transcription elongation-coupled chromatin remodeling / nucleus organization / spermatid development / histone demethylase activity / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / nucleosome binding / nucleosomal DNA binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / Inhibition of DNA recombination at telomere / methylated histone binding / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / FAD binding / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / 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 / HDMs demethylate histones / multicellular organism growth / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / male gonad development / NAD binding / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / NADP binding / Factors involved in megakaryocyte development and platelet production / flavin adenine dinucleotide binding / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / oxidoreductase activity / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å | ||||||
Authors | Chen, F. / Dong, Z. / Fang, J. / Yang, Y. / Li, Z. / Xu, Y. / Yang, H. / Wang, P. / Fang, R. / Shi, Y. / Xu, Y. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation Authors: Fang, R. / Chen, F. / Dong, Z. / Hu, D. / Barbera, A.J. / Clark, E.A. / Fang, J. / Yang, Y. / Mei, P. / Rutenberg, M. / Li, Z. / Zhang, Y. / Xu, Y. / Yang, H. / Wang, P. / Simon, M.D. / ...Authors: Fang, R. / Chen, F. / Dong, Z. / Hu, D. / Barbera, A.J. / Clark, E.A. / Fang, J. / Yang, Y. / Mei, P. / Rutenberg, M. / Li, Z. / Zhang, Y. / Xu, Y. / Yang, H. / Wang, P. / Simon, M.D. / Zhou, Q. / Li, J. / Marynick, M.P. / Li, X. / Lu, H. / Kaiser, U.B. / Kingston, R.E. / Xu, Y. / Shi, Y.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gur.cif.gz | 175.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gur.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gur_validation.pdf.gz | 743.6 KB | Display | wwPDB validaton report |
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Full document | 4gur_full_validation.pdf.gz | 759.2 KB | Display | |
Data in XML | 4gur_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 4gur_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/4gur ftp://data.pdbj.org/pub/pdb/validation_reports/gu/4gur | HTTPS FTP |
-Related structure data
Related structure data | 4gu1SC 4gusC 4gutC 4guuC 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: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q49A26, Oxidoreductases |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 2263.666 Da / Num. of mol.: 1 / Fragment: UNP residues 2-22 / Mutation: K4M / Source method: obtained synthetically / Details: H3K4 is mutated to Met / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243 |
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-Non-polymers , 4 types, 103 molecules
#4: Chemical | ChemComp-FAD / | ||
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#5: Chemical | ChemComp-GOL / | ||
#6: Chemical | #7: 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: 47.16 % |
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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: 0.97908 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2010 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 28816 / % possible obs: 88.57 % / Biso Wilson estimate: 39.29 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GU1 Resolution: 2.506→38.867 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8426 / SU ML: 0.3 / σ(F): 0.06 / Phase error: 22.9 / 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: 27.285 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.21 Å2 / Biso mean: 51.6845 Å2 / Biso min: 19.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.506→38.867 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: 11
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