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- PDB-1o0p: Solution Structure of the third RNA Recognition Motif (RRM) of U2... -

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Basic information

Entry
Database: PDB / ID: 1o0p
TitleSolution Structure of the third RNA Recognition Motif (RRM) of U2AF65 in complex with an N-terminal SF1 peptide
Components
  • Splicing Factor SF1
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA 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


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / spliceosomal complex assembly / mRNA 3'-splice site recognition / negative regulation of mRNA splicing, via spliceosome / Protein hydroxylation / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / spliceosomal complex / negative regulation of smooth muscle cell proliferation / mRNA splicing, via spliceosome / mRNA processing / transcription corepressor activity / nuclear speck / ribosome / mRNA binding / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / U2 snRNP auxilliary factor, large subunit, splicing factor / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RRM (RNA recognition motif) domain ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / U2 snRNP auxilliary factor, large subunit, splicing factor / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Splicing factor U2AF 65 kDa subunit / Splicing factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Restrained molecular dynamics using CNS, ARIA for ambiguous distance restraints
AuthorsSelenko, P. / Gregorovic, G. / Sprangers, R. / Stier, G. / Rhani, Z. / Kramer, A. / Sattler, M.
CitationJournal: 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
DepositionFeb 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit
B: Splicing Factor SF1


Theoretical massNumber of molelcules
Total (without water)13,6692
Polymers13,6692
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / U2 snRNP auxiliary factor large subunit / hU2AF(65)


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
#2: Protein/peptide Splicing Factor SF1


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
1213D 15N-separated NOESY
1323D 13C/15N-edited/filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM 15N,13C U2AF65-RRM3 + 1mM unlabeled SF1_10-25, 30mM phosphate buffer, 20mM NaCL, 3mM DTT90% H2O/10% D2O
21mM 15N,13C U2AF65-RRM3 + 1mM unlabeled SF1_10-25, 30mM phosphate buffer, 20mM NaCL, 3mM DTT100% D2O
Sample conditionsIonic strength: 50mM salt / pH: 6.4 / Pressure: ambient / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1DELAGIOprocessing
XEASYBARTELSdata analysis
ARIA1.2NILGESstructure solution
CNS1.1BRUNGERstructure solution
CNS1.1BRUNGERrefinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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