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- PDB-2rne: Solution structure of the second RNA recognition motif (RRM) of TIA-1 -

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Basic information

Entry
Database: PDB / ID: 2rne
TitleSolution structure of the second RNA recognition motif (RRM) of TIA-1
ComponentsTia1 protein
KeywordsRNA BINDING PROTEIN / RRM domain
Function / homology
Function and homology information


protein localization to cytoplasmic stress granule / nuclear stress granule / mRNA 3'-UTR AU-rich region binding / regulation of mRNA splicing, via spliceosome / negative regulation of cytokine production / positive regulation of epithelial cell apoptotic process / regulation of alternative mRNA splicing, via spliceosome / stress granule assembly / RNA splicing / mRNA 3'-UTR binding ...protein localization to cytoplasmic stress granule / nuclear stress granule / mRNA 3'-UTR AU-rich region binding / regulation of mRNA splicing, via spliceosome / negative regulation of cytokine production / positive regulation of epithelial cell apoptotic process / regulation of alternative mRNA splicing, via spliceosome / stress granule assembly / RNA splicing / mRNA 3'-UTR binding / mRNA processing / cytoplasmic stress granule / negative regulation of translation / ribonucleoprotein complex / apoptotic process / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TIA-1, RNA recognition motif 3 / TIA-1, RNA recognition motif 1 / TIA-1, RNA recognition motif 2 / TIAR, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...TIA-1, RNA recognition motif 3 / TIA-1, RNA recognition motif 1 / TIA-1, RNA recognition motif 2 / TIAR, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / 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
Cytotoxic granule associated RNA binding protein TIA1 / Nucleolysin TIA-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsT cell intracellular antigen-1 (TIA-1)
AuthorsTakahashi, M. / Kuwasako, K. / Abe, C. / Tsuda, K. / Inoue, M. / Terada, T. / Shirouzu, M. / Kobayashi, N. / Kigawa, T. / Taguchi, S. ...Takahashi, M. / Kuwasako, K. / Abe, C. / Tsuda, K. / Inoue, M. / Terada, T. / Shirouzu, M. / Kobayashi, N. / Kigawa, T. / Taguchi, S. / Guntert, P. / Hayashizaki, Y. / Tanaka, A. / Muto, Y. / Yokoyama, S.
CitationJournal: Biochemistry / Year: 2008
Title: Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode
Authors: Kuwasako, K. / Takahashi, M. / Tochio, N. / Abe, C. / Tsuda, K. / Inoue, M. / Terada, T. / Shirouzu, M. / Kobayashi, N. / Kigawa, T. / Taguchi, S. / Tanaka, A. / Hayashizaki, Y. / Guntert, P. ...Authors: Kuwasako, K. / Takahashi, M. / Tochio, N. / Abe, C. / Tsuda, K. / Inoue, M. / Terada, T. / Shirouzu, M. / Kobayashi, N. / Kigawa, T. / Taguchi, S. / Tanaka, A. / Hayashizaki, Y. / Guntert, P. / Muto, Y. / Yokoyama, S.
History
DepositionDec 19, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tia1 protein


Theoretical massNumber of molelcules
Total (without water)12,4331
Polymers12,4331
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tia1 protein /


Mass: 12432.717 Da / Num. of mol.: 1 / Fragment: RRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: Tia1 / References: UniProt: Q80ZW7, UniProt: P52912*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: T cell intracellular antigen-1 (TIA-1)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 20mM [U-99% 2H] TRIS, 100mM sodium chloride, 1mM [U-98% 2H] DTT, 0.02% sodium azide, 1mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRIS[U-99% 2H]1
100 mMsodium chloride1
1 mMDTT[U-98% 2H]1
0.02 %sodium azide1
1 mMprotein[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 100M / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameClassification
OPALstructure solution
OPALrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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