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Yorodumi- PDB-1o0p: Solution Structure of the third RNA Recognition Motif (RRM) of U2... -
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-Basic information
Entry | Database: PDB / ID: 1o0p | ||||||
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Title | Solution Structure of the third RNA Recognition Motif (RRM) of U2AF65 in complex with an N-terminal SF1 peptide | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / NON-CANONICAL RNA RECOGNITION MOTIF / 4-STRANDED ANTI-PARALLEL BETA-SHEET / 2 ALPHA HELICES additionally extended by a third helix C | ||||||
Function / homology | Function and homology information nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Leydig cell differentiation / male sex determination / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding ...nuclear body organization / U2AF complex / regulation of steroid biosynthetic process / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Leydig cell differentiation / male sex determination / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / spliceosomal complex assembly / molecular function inhibitor activity / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / mRNA 3'-splice site recognition / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / negative regulation of smooth muscle cell proliferation / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / transcription corepressor activity / nuclear body / ribosome / nuclear speck / mRNA binding / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Restrained molecular dynamics using CNS, ARIA for ambiguous distance restraints | ||||||
Authors | Selenko, P. / Gregorovic, G. / Sprangers, R. / Stier, G. / Rhani, Z. / Kramer, A. / Sattler, M. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Structural Basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP Authors: Selenko, P. / Gregorovic, G. / Sprangers, R. / Stier, G. / Rhani, Z. / Kramer, A. / Sattler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o0p.cif.gz | 370.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o0p.ent.gz | 318.4 KB | Display | PDB format |
PDBx/mmJSON format | 1o0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/1o0p ftp://data.pdbj.org/pub/pdb/validation_reports/o0/1o0p | HTTPS FTP |
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-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 | Mass: 11976.615 Da / Num. of mol.: 1 / Fragment: C-terminal RRM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: modified pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P26368 |
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#2: Protein/peptide | Mass: 1691.936 Da / Num. of mol.: 1 / Fragment: N-terminal peptide / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED AND DERIVED FROM THE N-TERMINUS OF SF1. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN). References: GenBank: 2463198, UniProt: Q15637*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 50mM salt / pH: 6.4 / Pressure: ambient / Temperature: 295 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Restrained molecular dynamics using CNS, ARIA for ambiguous distance restraints Software ordinal: 1 Details: THE EXPERIMENTALLY DETERMINED DISTANCE (3232 NOEs, INCLUDING 258 FOR THE SF1 PEPTIDE, 64 INTERMOLECULAR, AND 2*35 FOR HYDROGEN BONDS) AND DIHEDRAL ANGLE RESTRAINTS (99) WERE APPLIED IN A ...Details: THE EXPERIMENTALLY DETERMINED DISTANCE (3232 NOEs, INCLUDING 258 FOR THE SF1 PEPTIDE, 64 INTERMOLECULAR, AND 2*35 FOR HYDROGEN BONDS) AND DIHEDRAL ANGLE RESTRAINTS (99) WERE APPLIED IN A MIXED TORSION AND CARTESIAN ANGLE DYNAMICS/SIMULATED ANNEALING PROTOCOL. STRUCTURAL QUALITY WAS ASSESED WITH PROCHECK. | ||||||||||||||||||||||||
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: 10 |