+Open data
-Basic information
Entry | Database: PDB / ID: 4fwf | ||||||
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Title | Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic | ||||||
Components |
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Keywords | OXIDOREDUCTASE/PROTEIN BINDING / lsd2 / fad / histone demethylase / C4H2C2 / CW / histone / epigenetic / OXIDOREDUCTASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information epigenetic programing of female pronucleus / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / telomere organization ...epigenetic programing of female pronucleus / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / 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) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / 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 / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / flavin adenine dinucleotide binding / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / oxidoreductase activity / cadherin binding / protein heterodimerization activity / 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 / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Zhang, Q. / Chen, Z. | ||||||
Citation | Journal: Cell Res. / Year: 2013 Title: Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b Authors: Zhang, Q. / Qi, S. / Xu, M. / Yu, L. / Tao, Y. / Deng, Z. / Wu, W. / Li, J. / Chen, Z. / Wong, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fwf.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fwf.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 4fwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fwf_validation.pdf.gz | 719.1 KB | Display | wwPDB validaton report |
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Full document | 4fwf_full_validation.pdf.gz | 729.4 KB | Display | |
Data in XML | 4fwf_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 4fwf_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/4fwf ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fwf | HTTPS FTP |
-Related structure data
Related structure data | 4fweSC 4fwjC 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
#1: Protein | Mass: 89340.977 Da / Num. of mol.: 1 / Fragment: UNP residues 30-822 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LSD2 / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 / References: UniProt: Q8NB78, Oxidoreductases | ||||
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#2: Protein/peptide | Mass: 2192.588 Da / Num. of mol.: 1 / Fragment: UNP residues 2-21 / Mutation: K4M / Source method: obtained synthetically / Details: chain E are synthesized from company / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431 | ||||
#3: Chemical | #4: Chemical | ChemComp-FAD / | #5: 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: 3 Å3/Da / Density % sol: 58.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 21% PEG3350, 200mM diammonium citrate, pH 7, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 31359 / Num. obs: 30975 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.072 / Rsym value: 0.054 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1509 / Rsym value: 0.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FWE Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.811 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.788 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 41.283 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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