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Yorodumi- PDB-2dt7: Solution structure of the second SURP domain of human splicing fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dt7 | ||||||
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Title | Solution structure of the second SURP domain of human splicing factor SF3a120 in complex with a fragment of human splicing factor SF3a60 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / structure genomics / SF3a120 / SF3a60 / SURP domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information RNA splicing, via transesterification reactions / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway ...RNA splicing, via transesterification reactions / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS, restrained ENERGY MINIMIZATION | ||||||
Authors | He, F. / Kuwasako, K. / Inoue, M. / Guntert, P. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Structure / Year: 2006 Title: Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP Authors: Kuwasako, K. / He, F. / Inoue, M. / Tanaka, A. / Sugano, S. / Guentert, P. / Muto, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dt7.cif.gz | 780.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dt7.ent.gz | 657.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dt7_validation.pdf.gz | 364.6 KB | Display | wwPDB validaton report |
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Full document | 2dt7_full_validation.pdf.gz | 552.6 KB | Display | |
Data in XML | 2dt7_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 2dt7_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/2dt7 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/2dt7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4452.058 Da / Num. of mol.: 1 / Fragment: residues 70-107 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF3a60, SF3a3 Plasmid: PGEX6P-1-SF3A60 (71-107)-HIS(6)-SF3A120 SURP2 (134-217) Production host: Escherichia coli (E. coli) / References: UniProt: Q12874 |
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#2: Protein | Mass: 9990.318 Da / Num. of mol.: 1 / Fragment: SURP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF3a120/SF3a1 Plasmid: PGEX6P-1-SF3A60 (71-107)-HIS(6)-SF3A120 SURP2 (134-217) Production host: Escherichia coli (E. coli) / References: UniProt: Q15459 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 2.0mM U-15N, 13C PROTEIN; 20mM sodium phosphate; 1mM d-DTT; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 20mM / pH: 6 / Pressure: AMBIENT / Temperature: 308 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS, restrained ENERGY MINIMIZATION Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |