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Yorodumi- PDB-2rje: Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 1... -
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-Basic information
Entry | Database: PDB / ID: 2rje | ||||||
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Title | Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), orthorhombic form II | ||||||
Components |
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Keywords | TRANSCRIPTION / L(3)MBT-LIKE PROTEIN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription regulation / Zinc-finger / Chromosomal protein / Methylation / Nucleosome core | ||||||
Function / homology | Function and homology information SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin formation / Packaging Of Telomere Ends / condensed chromosome / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / methylated histone binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / 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 / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / HDMs demethylate histones / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / Regulation of TP53 Activity through Methylation / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / 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 / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / regulation of cell cycle / protein heterodimerization activity / Amyloid fiber formation / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Allali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. ...Allali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J.R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: L3MBTL1 recognition of mono- and dimethylated histones. Authors: Min, J. / Allali-Hassani, A. / Nady, N. / Qi, C. / Ouyang, H. / Liu, Y. / MacKenzie, F. / Vedadi, M. / Arrowsmith, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rje.cif.gz | 222.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rje.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 2rje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/2rje ftp://data.pdbj.org/pub/pdb/validation_reports/rj/2rje | HTTPS FTP |
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-Related structure data
Related structure data | 2pqwSC 2rjcC 2rjdC 2rjfC 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37751.211 Da / Num. of mol.: 3 / Fragment: Residues 200-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pET28a-mhl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y468 #2: Protein/peptide | Mass: 1425.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P62805*PLUS #3: Chemical | #4: 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: 2.66 Å3/Da / Density % sol: 53.68 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 6% PEG 3350, 0.1M Ammonium sulfate, 20% Glycerol, 0.1 M Sodium acetate pH 4.4 , VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 18, 2006 / Details: varimax |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→37.48 Å / Num. all: 103400 / Num. obs: 103400 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.085 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PQW Resolution: 1.86→37.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.02 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.538 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→37.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.91 Å / Total num. of bins used: 20
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