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Yorodumi- PDB-7vh9: Solution structure of the chimeric peptide of the first SURP doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vh9 | ||||||||||||
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Title | Solution structure of the chimeric peptide of the first SURP domain of Human SF3A1 and the interacting region of SF1. | ||||||||||||
Components | Splicing factor 3A subunit 1,Splicing factor 1 | ||||||||||||
Keywords | SPLICING / SURP / U2 snRNP / SF3A1 / SF1 | ||||||||||||
Function / homology | Function and homology information nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type prespliceosome assembly ...nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / Leydig cell differentiation / male sex determination / regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / negative regulation of smooth muscle cell proliferation / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / transcription corepressor activity / nuclear body / ribosome / nuclear speck / mRNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | SOLUTION NMR / molecular dynamics | ||||||||||||
Authors | Muto, Y. / Kuwasako, K. / Takizawa, M. / Kobayashi, N. / Sakamoto, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1. Authors: Nameki, N. / Takizawa, M. / Suzuki, T. / Tani, S. / Kobayashi, N. / Sakamoto, T. / Muto, Y. / Kuwasako, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vh9.cif.gz | 646.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vh9.ent.gz | 542.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vh9_validation.pdf.gz | 396.3 KB | Display | wwPDB validaton report |
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Full document | 7vh9_full_validation.pdf.gz | 495.9 KB | Display | |
Data in XML | 7vh9_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 7vh9_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/7vh9 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/7vh9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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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: 12133.198 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SF3A1, SAP114, SF1, ZFM1, ZNF162 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15459, UniProt: Q15637 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Sample state: isotropic / Type: 3D 13C,15N-SEPARATED NOESY SPECTRA |
-Sample preparation
Details | Type: solution Contents: 1.4 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O Details: 20 mM sodium phosphate buffer (pH 7.0); 1mM D-DTT;0.02% NaN3 were used to keep the protein condition Label: 13C,15N_sample / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.4 mM / Component: protein / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Details: 20 mM sodium phosphate buffer (pH 7.0); 1mM D-DTT; 0.02% NaN3 Ionic strength: 20 mM / Label: condition_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |