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Yorodumi- PDB-2v89: Crystal structure of RAG2-PHD finger in complex with H3K4me3 pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v89 | |||||||||
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Title | Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution | |||||||||
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 / TRIMETHYL LYSINE / DNA RECOMBINATION | |||||||||
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 / telomere organization / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / phosphatidylinositol-4,5-bisphosphate binding / Assembly of the ORC complex at the origin of replication / methylated histone binding / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / phosphatidylinositol binding / Condensation of Prophase Chromosomes / HCMV Late Events / B cell differentiation / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / 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 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / ubiquitin protein ligase activity / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / T cell differentiation in thymus / Oxidative Stress Induced Senescence / sequence-specific DNA binding / DNA recombination / Estrogen-dependent gene expression / defense response to bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||
Authors | Ramon-Maiques, S. / Yang, W. | |||||||||
Citation | 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. #1: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v89.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v89.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v89_validation.pdf.gz | 467.7 KB | Display | wwPDB validaton report |
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Full document | 2v89_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 2v89_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2v89_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/2v89 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v89 | HTTPS FTP |
-Related structure data
Related structure data | 2v83S 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: 1090.296 Da / Num. of mol.: 2 / Fragment: H3 (1-21), BIOTINYLATED AT C-TERMINUS / Source method: obtained synthetically / Details: TRI-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: 2.21 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: CRYSTALS OF COMPLEX WERE OBTAINED AT 3 MG/ML PROTEIN CONCENTRATION AND 1:1.5 MOLAR RATIO OF PROTEIN TO PEPTIDE USING HANGING DROP AND VAPOR DIFFUSION TECHNIQUE AT 293K. PRECIPITANT SOLUTION: ...Details: CRYSTALS OF COMPLEX WERE OBTAINED AT 3 MG/ML PROTEIN CONCENTRATION AND 1:1.5 MOLAR RATIO OF PROTEIN TO PEPTIDE USING HANGING DROP AND VAPOR DIFFUSION TECHNIQUE AT 293K. PRECIPITANT SOLUTION: 26% PEG 3350, 0.18M POTASSIUM THIOCYANATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 4, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 75608 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 67.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V83 Resolution: 1.1→50 Å / Num. parameters: 15567 / Num. restraintsaints: 18875 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1233.3 / Occupancy sum non hydrogen: 1651.2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→50 Å
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Refine LS restraints |
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