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- PDB-2kxn: NMR structure of human Tra2beta1 RRM in complex with AAGAAC RNA -

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Basic information

Entry
Database: PDB / ID: 2kxn
TitleNMR structure of human Tra2beta1 RRM in complex with AAGAAC RNA
Components
  • 5'-R(*AP*AP*GP*AP*AP*C)-3'
  • Transformer-2 protein homolog beta
KeywordsRNA binding protein/RNA / SR protein / RRM / splicing factor / RNA protein complex / SMN / RNA binding protein-RNA complex
Function / homology
Function and homology information


cerebral cortex regionalization / embryonic brain development / pre-mRNA binding / RNA splicing, via transesterification reactions / positive regulation of mRNA splicing, via spliceosome / RHOBTB1 GTPase cycle / nuclear inner membrane / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA ...cerebral cortex regionalization / embryonic brain development / pre-mRNA binding / RNA splicing, via transesterification reactions / positive regulation of mRNA splicing, via spliceosome / RHOBTB1 GTPase cycle / nuclear inner membrane / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RHOBTB2 GTPase cycle / mRNA Splicing - Major Pathway / cellular response to glucose stimulus / spliceosomal complex / mRNA splicing, via spliceosome / protein domain specific binding / mRNA binding / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Transformer-2 protein homolog beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsClery, A. / Jayne, S. / Benderska, N. / Dominguez, C. / Stamm, S. / Allain, F.H.-T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-beta1
Authors: Clery, A. / Jayne, S. / Benderska, N. / Dominguez, C. / Stamm, S. / Allain, F.H.
History
DepositionMay 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*AP*AP*GP*AP*AP*C)-3'
B: Transformer-2 protein homolog beta


Theoretical massNumber of molelcules
Total (without water)16,4192
Polymers16,4192
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)12 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 1922.253 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Transformer-2 protein homolog beta / / TRA-2 beta / TRA2-beta / hTRA2-beta / Transformer-2 protein homolog B / Splicing factor / ...TRA-2 beta / TRA2-beta / hTRA2-beta / Transformer-2 protein homolog B / Splicing factor / arginine/serine-rich 10


Mass: 14497.215 Da / Num. of mol.: 1 / Fragment: RRM domain, residues 106-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA2B, SFRS10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62995

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HNCA
1612D 1H-1H TOCSY
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HN(CA)CB

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Sample preparation

DetailsContents: 0.8 mM [U-15N] Tra2beta1-1, 0.8 mM [U-13C; U-15N] Tra2beta1-2, 0.8 mM RNA (5'-R(*AP*AP*GP*AP*AP*C)-3')-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMTra2beta1-1[U-15N]1
0.8 mMTra2beta1-2[U-13C; U-15N]1
0.8 mMRNA (5'-R(*AP*AP*GP*AP*AP*C)-3')-31
Sample conditionsIonic strength: 120 / pH: 5.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.113Goddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 12

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