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Yorodumi- PDB-2do4: Solution structure of the RNA binding domain of squamous cell car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2do4 | ||||||
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Title | Solution structure of the RNA binding domain of squamous cell carcinoma antigen recognized by T cells 3 | ||||||
Components | Squamous cell carcinoma antigen recognized by T-cells 3 | ||||||
Keywords | IMMUNE SYSTEM / RRM domaim / RDB / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information U6atac snRNA binding / ASAP complex / U4 snRNA binding / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / Cajal body ...U6atac snRNA binding / ASAP complex / U4 snRNA binding / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / Cajal body / spliceosomal snRNP assembly / cell morphogenesis / mRNA splicing, via spliceosome / nucleosome assembly / histone binding / regulation of gene expression / nuclear speck / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dyanamics, simulated annealing | ||||||
Authors | Tanabe, W. / Suzuki, S. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the RNA binding domain of squamous cell carcinoma antigen recognized by T cells 3 Authors: Suzuki, S. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2do4.cif.gz | 588.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2do4.ent.gz | 493.1 KB | Display | PDB format |
PDBx/mmJSON format | 2do4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2do4_validation.pdf.gz | 340.6 KB | Display | wwPDB validaton report |
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Full document | 2do4_full_validation.pdf.gz | 473.1 KB | Display | |
Data in XML | 2do4_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 2do4_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/2do4 ftp://data.pdbj.org/pub/pdb/validation_reports/do/2do4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10772.243 Da / Num. of mol.: 1 / Fragment: RNA recognition motif Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: SART3 / Plasmid: P051121-11 / References: UniProt: Q15020 |
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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: 1.1mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / 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 dyanamics, simulated annealing / 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 |