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- PDB-2i38: Solution structure of the RRM of SRp20 -

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Basic information

Entry
Database: PDB / ID: 2i38
TitleSolution structure of the RRM of SRp20
ComponentsFusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3
KeywordsRNA BINDING PROTEIN/CHIMERA / RRM / alpha-beta sandwich / beta1-alpha1-beta2-beta3-alpha2-beta4 / RNA BINDING PROTEIN-CHIMERA COMPLEX
Function / homology
Function and homology information


primary miRNA binding / primary miRNA processing / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / IgG binding / phospholipase binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA export from nucleus ...primary miRNA binding / primary miRNA processing / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / IgG binding / phospholipase binding / Processing of Capped Intron-Containing Pre-mRNA / mRNA export from nucleus / cellular response to leukemia inhibitory factor / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / nuclear speck / RNA binding / extracellular region / nucleoplasm / cytoplasm
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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
Immunoglobulin G-binding protein G / Serine/arginine-rich splicing factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SANDER module of AMBER 7
AuthorsHargous, Y.F. / Allain, F.H.T.
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 1.3Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name
Revision 1.4Oct 20, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3


Theoretical massNumber of molelcules
Total (without water)16,8471
Polymers16,8471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Antibody Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3 / / Pre-mRNA-splicing factor SRP20


Mass: 16846.656 Da / Num. of mol.: 1 / Fragment: RRM domain / Mutation: E129D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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
1122D NOESY
121HNCA
131CBCA(CO)NH
1423D 15N-separated NOESY
1513D 13C-separated NOESY
161(H)CCH TOCSY
1722D 1H-15N HSQC
1822D TOCSY
1912D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM SRp20 13C-15N labelled in 50 mM sodium dihydrogenophosphate, pH 5.8, 1mM DTT;10% D2O, 90% H2O or 100% D2O
21mM SRp20 15N labelled in 50 mM sodium dihydrogenophosphate, pH 5.8, 1mM DTT;10% D2O, 90% H2O or 100% D2O
Sample conditionspH: 5.8 / 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 DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameDeveloperClassification
DYANAstructure solution
Sparkydata analysis
Amber 7Case and Cornellrefinement
RefinementMethod: SANDER module of AMBER 7 / Software ordinal: 1 / Details: generalized-Born solvation model
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 19

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