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Yorodumi- PDB-2v86: Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v86 | |||||||||
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Title | Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide | |||||||||
Components |
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Keywords | PROTEIN BINDING / V(D)J RECOMBINATION / COVALENT MODIFICATIONS / RAG2 / HISTONE / NUCLEUS / NUCLEASE / HYDROLASE / PHD FINGER / DNA-BINDING / RECOMBINASE / ENDONUCLEASE / TRIMETHYL LYSINE / DIMETHYL ARGININE / DNA RECOMBINATION | |||||||||
Function / homology | Function and homology information Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / mature B cell differentiation involved in immune response / PRC2 methylates histones and DNA / HATs acetylate histones / DNA recombinase complex / PKMTs methylate histone lysines / B cell homeostatic proliferation / DN2 thymocyte differentiation ...Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / mature B cell differentiation involved in immune response / PRC2 methylates histones and DNA / HATs acetylate histones / DNA recombinase complex / PKMTs methylate histone lysines / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / pre-B cell allelic exclusion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / positive regulation of organ growth / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / V(D)J recombination / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / organ growth / T cell lineage commitment / B cell lineage commitment / phosphatidylinositol-3,4,5-trisphosphate binding / T cell differentiation / epigenetic regulation of gene expression / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / B cell differentiation / nucleosome assembly / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / T cell differentiation in thymus / gene expression / chromatin organization / DNA recombination / sequence-specific DNA binding / defense response to bacterium / protein heterodimerization activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Ramon-Maiques, S. / Yang, W. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2. Authors: Ramon-Maiques, S. / Kuo, A.J. / Carney, D. / Matthews, A.G.W. / Oettinger, M.A. / Gozani, O. / Yang, W. #1: Journal: Nature / Year: 2007 Title: Rag2 Phd Finger Couples Histone H3 Lysine 4 Trimethylation with V(D)J Recombination. Authors: Matthews, A.G.W. / Kuo, A.J. / Ramon-Maiques, S. / Han, S. / Champagne, K.S. / Ivanov, D. / Gallardo, M. / Carney, D. / Cheung, P. / Ciccone, D.N. / Walter, K.L. / Utz, P.J. / Shi, Y. / ...Authors: Matthews, A.G.W. / Kuo, A.J. / Ramon-Maiques, S. / Han, S. / Champagne, K.S. / Ivanov, D. / Gallardo, M. / Carney, D. / Cheung, P. / Ciccone, D.N. / Walter, K.L. / Utz, P.J. / Shi, Y. / Kutateladze, T.G. / Yang, W. / Gozani, O. / Oettinger, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v86.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v86.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/2v86 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v86 | HTTPS FTP |
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-Related structure data
Related structure data | 2v83SC 2v85C 2v87C 2v88C 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: 9360.498 Da / Num. of mol.: 2 / Fragment: RESIDUES 414-487 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21784 #2: Protein/peptide | Mass: 1074.277 Da / Num. of mol.: 2 / Fragment: H3 (1-21), BIOTINILATED AT C-TERMINUS / Source method: obtained synthetically Details: R2 ASYMMETRICALLY DIMETHYLATED AND K4 TRIMETHYLATED Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P84228 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Sequence details | N-TERMINAL SEGMENT GPLGSPEFG IS CARRIED OVER FROM THE EXPRESSION | |
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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: 2.23 Å3/Da / Density % sol: 44.48 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: VAPOR DIFFUSION. HANGING DROP. 28% PEG 20,000, 0.1M MES PH 6.5, 3% ISOPROPANOL TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Mar 4, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 11827 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V83 Resolution: 2.05→30 Å / Rfactor Rfree error: 0.00087 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.2446 Å2 / ksol: 0.360332 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.496 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 11
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