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Yorodumi- PDB-2dnv: Solution Structure of RSGI RUH-055, a Chromo Domain from Mus musc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dnv | ||||||
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Title | Solution Structure of RSGI RUH-055, a Chromo Domain from Mus musculus cDNA | ||||||
Components | Chromobox protein homolog 8 | ||||||
Keywords | TRANSCRIPTION / Chromo domain / Histone H3 tail / Choromatin organization modifier / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information : / SUMOylation of RNA binding proteins / Regulation of PTEN gene transcription / SUMOylation of DNA damage response and repair proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / heterochromatin formation => GO:0031507 / PRC1 complex / ubiquitin-protein transferase activator activity ...: / SUMOylation of RNA binding proteins / Regulation of PTEN gene transcription / SUMOylation of DNA damage response and repair proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / heterochromatin formation => GO:0031507 / PRC1 complex / ubiquitin-protein transferase activator activity / chromatin => GO:0000785 / PcG protein complex / positive regulation of collagen biosynthetic process / heterochromatin / ubiquitin ligase complex / methylated histone binding / positive regulation of DNA repair / cellular response to hydrogen peroxide / single-stranded RNA binding / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Ruhul Momen, A.Z.M. / Hirota, H. / Tomizawa, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution Structure of RSGI RUH-055, a Chromo Domain from Mus musculus cDNA Authors: Ruhul Momen, A.Z.M. / Hirota, H. / Tomizawa, T. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dnv.cif.gz | 358.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dnv.ent.gz | 308.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/2dnv ftp://data.pdbj.org/pub/pdb/validation_reports/dn/2dnv | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7187.098 Da / Num. of mol.: 1 / Fragment: Methylated histone H3 tail binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Plasmid: P050711-03 / Production host: Cell free synthesis / References: UniProt: Q9QXV1 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.53mM domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM NaCl / pH: 7.0 / Pressure: Ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |