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- PDB-2kn4: The structure of the RRM domain of SC35 -

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Basic information

Entry
Database: PDB / ID: 2kn4
TitleThe structure of the RRM domain of SC35
ComponentsImmunoglobulin G-binding protein G,Serine/arginine-rich splicing factor 2
KeywordsRNA BINDING PROTEIN / RRM domain / Cell wall / IgG-binding protein / Peptidoglycan-anchor / Secreted / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


interchromatin granule / perichromatin fibrils / pre-mRNA binding / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / IgG binding / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA ...interchromatin granule / perichromatin fibrils / pre-mRNA binding / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / IgG binding / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / response to vitamin E / mRNA Splicing - Major Pathway / protein kinase C binding / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / transcription corepressor activity / nuclear speck / RNA binding / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
IgG-binding B / B domain / RNA recognition motif domain, eukaryote / RNA recognition motif / 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 ...IgG-binding B / B domain / RNA recognition motif domain, eukaryote / RNA recognition motif / 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 2
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsClayton, J.C. / Goult, B.T. / Lian, L.-Y.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: The structure and selectivity of the SR protein SRSF2 RRM domain with RNA
Authors: Phelan, M.M. / Goult, B.T. / Clayton, J.C. / Hautbergue, G.M. / Wilson, S.A. / Lian, L.-Y.
History
DepositionAug 14, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Feb 12, 2020Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref.db_code / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G,Serine/arginine-rich splicing factor 2


Theoretical massNumber of molelcules
Total (without water)18,1331
Polymers18,1331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G-binding protein G,Serine/arginine-rich splicing factor 2 / IgG-binding protein G / Protein PR264 / Splicing component / 35 kDa / Splicing factor SC35 / SC-35 ...IgG-binding protein G / Protein PR264 / Splicing component / 35 kDa / Splicing factor SC35 / SC-35 / Splicing factor / arginine/serine-rich 2


Mass: 18133.104 Da / Num. of mol.: 1
Fragment: UNP residues 304-357 from P19909, UNP residues 9-101 from Q01130
Source method: isolated from a genetically manipulated source
Details: Chimera of Immunoglobulin G-binding protein G, linker, Splicing factor; arginine/serine-rich 2
Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human)
Gene: spg, SRSF2, SFRS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19909, UniProt: Q01130

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D HBHANH
11023D (H)CCH-TOCSY
11142D 1H-1H TOCSY
11242D 1H-1H NOESY
11333D 1H-15N NOESY
11413D 1H-13C NOESY
11523D 1H-13C NOESY
11613D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] SC35-1, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] SC35-2, 100% D2O100% D2O
30.5 mM [U-100% 15N] SC35-3, 90% H2O/10% D2O90% H2O/10% D2O
40.5 mM SC35-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMSC35-1[U-100% 13C; U-100% 15N]1
0.5 mMSC35-2[U-100% 13C; U-100% 15N]2
0.5 mMSC35-3[U-100% 15N]3
0.5 mMSC35-44
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CCPN_Analysis1CCPNchemical shift assignment
CCPN_Analysis1CCPNdata analysis
CCPN_Analysis1CCPNpeak picking
ARIA1.2Linge, O'Donoghue and Nilgesgeometry optimization
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
CYANA2Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: FINAL STRUCTURES REFINED IN EXPLICIT WATER BATH AS IMPLEMENTED IN ARIA 1.2/CNS 1.1. 20 LOWEST ENERGY STRUCTURES SELECTED FROM WATER REFINEMENT USING CNS. INITIAL STRUCTURES GENERATED WITH CYANA
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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