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- PDB-2i2y: Solution structure of the RRM of SRp20 bound to the RNA CAUC -

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Basic information

Entry
Database: PDB / ID: 2i2y
TitleSolution structure of the RRM of SRp20 bound to the RNA CAUC
Components
  • (5'-R(*CP*AP*UP*C)-3')
  • Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3
KeywordsRNA binding protein/Chimera/RNA / PROTEIN-RNA COMPLEX RRM alpha-beta sandwich beta1-alpha1-beta2-beta3-alpha2-beta4 / RNA binding protein-Chimera-RNA COMPLEX
Function / homology
Function and homology information


protein-RNA sequence-specific adaptor activity / primary miRNA binding / primary miRNA processing / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / IgG binding / RNA Polymerase II Transcription Termination / phospholipase binding ...protein-RNA sequence-specific adaptor activity / primary miRNA binding / primary miRNA processing / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / IgG binding / RNA Polymerase II Transcription Termination / phospholipase binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA export from nucleus / mRNA Splicing - Major Pathway / cellular response to leukemia inhibitory factor / nuclear speck / mRNA binding / RNA binding / extracellular region / nucleoplasm / cytoplasm
Similarity search - Function
: / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif ...: / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / 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 / Ubiquitin-like (UB roll) / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Immunoglobulin G-binding protein G / Serine/arginine-rich splicing factor 3
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / AMBER 7
AuthorsHargous, Y.F. / Allain, F.H.
CitationJournal: Embo J. / Year: 2006
Title: Molecular basis of RNA recognition and TAP binding by the SR proteins SRp20 and 9G8.
Authors: Hargous, Y. / Hautbergue, G.M. / Tintaru, A.M. / Skrisovska, L. / Golovanov, A.P. / Stevenin, J. / Lian, L.Y. / Wilson, S.A. / Allain, F.H.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: (5'-R(*CP*AP*UP*C)-3')
A: Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3


Theoretical massNumber of molelcules
Total (without water)18,0612
Polymers18,0612
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)28 / 50structures with the least restraint violations
Representative

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Components

#1: RNA chain (5'-R(*CP*AP*UP*C)-3')


Mass: 1200.778 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: core sequence of exonic splicing enhancers recognised by SRp20
#2: Antibody Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3 / Pre-mRNA-splicing factor SRP20


Mass: 16860.682 Da / Num. of mol.: 1 / Fragment: RRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G', Homo sapiens
Genus: Streptococcus, Homo / Species: , / Strain: , / Gene: spg and SFRS3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+ RIL / References: UniProt: P19909, UniProt: P84103

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121CBCA(CO)NH
1313D 13C-separated NOESY
1423D 15N-separated NOESY
151(H)CCH TOCSY
1622D NOESY
1722D TOCSY
1833D flitered [1H,13C,1H] NOESY
1912D filtered/edited NOESY
1101

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM SRp20 13C-15N labelled + 1 mM CAUC natural abundance in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT;10% D2O,90% H2O or 100% D2O
21mM SRp20 15N labelled + 1 mM CAUC natural abundance in 1mM SRp20 15N labelled in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT10% D2O, 90% H2O or 100% D2O
31mM SRp20 15N labelled + 1 mM CAUC with 13C labelled riboses and natural abundance bases in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT;10% D2O, 90% H2O or 100% D2O
41mM SRp20 15N labelled + 1 mM CAUC with A2 and U3 riboses 13C labelled and natural abundance of other riboses and all bases in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT;10% D2O, 90% H2O or 100% D2O
51mM SRp20 15N labelled + 1 mM CAUC with C1 and C4 riboses 13C labelled and natural abundance of other riboses and all bases, in 50 mM sodium dihydrogenophosphate, pH 6.4, 1mM DTT;10% D2O, 90% H2O or 100% D2O
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 315 K

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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 DRXBrukerDRX9001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameDeveloperClassification
DIANAstructure solution
Sparkydata analysis
Amber 7Case and Cornellrefinement
RefinementMethod: AMBER 7 / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 28

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