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Yorodumi- PDB-2v88: Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v88 | ||||||
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Title | Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / V(D)J RECOMBINATION / COVALENT MODIFICATIONS / RAG / HISTONE / NUCLEUS / NUCLEASE / HYDROLASE / PHD FINGER / DNA-BINDING / RECOMBINASE / ENDONUCLEASE / DIMETHYL LYSINE / DNA RECOMBINATION / SYMMETRIC DIMETHYLATED ARGININE | ||||||
Function / homology | Function and homology information mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding ...mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / pre-B cell allelic exclusion / positive regulation of organ growth / 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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / phosphatidylinositol binding / Assembly of the ORC complex at the origin of replication / DNA methylation / B cell differentiation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / gene expression / T cell differentiation in thymus / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / sequence-specific DNA binding / defense response to bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 | 2v88.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v88.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 2v88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/2v88 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v88 | HTTPS FTP |
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-Related structure data
Related structure data | 2v83SC 2v85C 2v86C 2v87C C: citing same article (ref.) S: Starting model for refinement |
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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: 902.050 Da / Num. of mol.: 2 / Fragment: H3 (1-21), BIOTINYLATED AT C-TERMINUS / Source method: obtained synthetically / Details: SYMMETRIC DI-METHYLATED R2 AND DI-METHYLATED K4 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q5TEC6, UniProt: P68431*PLUS #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: 2.42 Å3/Da / Density % sol: 48.78 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM POTASSIUM FLUORIDE. 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: Oct 6, 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→30 Å / Num. obs: 12678 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V83 Resolution: 2→30 Å / Rfactor Rfree error: 0.009 / 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: 52.9399 Å2 / ksol: 0.365658 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.222 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.06 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 12
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