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Yorodumi- PDB-5gvq: Solution structure of the first RRM domain of human spliceosomal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gvq | |||||||||
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Title | Solution structure of the first RRM domain of human spliceosomal protein SF3b49 | |||||||||
Components | Splicing factor 3B subunit 4 | |||||||||
Keywords | RNA BINDING PROTEIN / RRM / SF3b49 / SF3b145 / U2 snRNP / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information U2-type prespliceosome assembly / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / U2 snRNP / mRNA Splicing - Minor Pathway / spliceosomal complex ...U2-type prespliceosome assembly / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / U2 snRNP / mRNA Splicing - Minor Pathway / spliceosomal complex / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / mRNA processing / RNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Kuwasako, K. / Nameki, N. / Tsuda, K. / Takahashi, M. / Sato, A. / Tochio, N. / Inoue, M. / Terada, T. / Kigawa, T. / Kobayashi, N. ...Kuwasako, K. / Nameki, N. / Tsuda, K. / Takahashi, M. / Sato, A. / Tochio, N. / Inoue, M. / Terada, T. / Kigawa, T. / Kobayashi, N. / Shirouzu, M. / Ito, T. / Sakamoto, T. / Wakamatsu, K. / Guntert, P. / Takahashi, S. / Yokoyama, S. / Muto, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: Protein Sci. / Year: 2017 Title: Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment. Authors: Kuwasako, K. / Nameki, N. / Tsuda, K. / Takahashi, M. / Sato, A. / Tochio, N. / Inoue, M. / Terada, T. / Kigawa, T. / Kobayashi, N. / Shirouzu, M. / Ito, T. / Sakamoto, T. / Wakamatsu, K. / ...Authors: Kuwasako, K. / Nameki, N. / Tsuda, K. / Takahashi, M. / Sato, A. / Tochio, N. / Inoue, M. / Terada, T. / Kigawa, T. / Kobayashi, N. / Shirouzu, M. / Ito, T. / Sakamoto, T. / Wakamatsu, K. / Guntert, P. / Takahashi, S. / Yokoyama, S. / Muto, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gvq.cif.gz | 611.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gvq.ent.gz | 531.7 KB | Display | PDB format |
PDBx/mmJSON format | 5gvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/5gvq ftp://data.pdbj.org/pub/pdb/validation_reports/gv/5gvq | 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: 11378.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B4, SAP49 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15427*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.8 mM [U-100% 13C; U-100% 15N] human spliceosomal protein SF3b49, 90% H2O/10% D2O Label: sample_1 / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.8 mM / Component: human spliceosomal protein SF3b49 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 100 mM / Label: condistions_1 / pH: 7.0 / Pressure: 1 atm / 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: simulated annealing / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |