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- PDB-2mjn: Structure, dynamics and RNA binding of the multi-domain splicing ... -

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Basic information

Entry
Database: PDB / ID: 2mjn
TitleStructure, dynamics and RNA binding of the multi-domain splicing factor TIA-1
ComponentsNucleolysin TIA-1 isoform p40
KeywordsRNA BINDING PROTEIN / RRM / TIA-1
Function / homology
Function and homology information


protein localization to cytoplasmic stress granule / nuclear stress granule / mRNA 3'-UTR AU-rich region binding / poly(A) binding / regulation of mRNA splicing, via spliceosome / positive regulation of epithelial cell apoptotic process / FGFR2 alternative splicing / negative regulation of cytokine production / regulation of alternative mRNA splicing, via spliceosome / stress granule assembly ...protein localization to cytoplasmic stress granule / nuclear stress granule / mRNA 3'-UTR AU-rich region binding / poly(A) binding / regulation of mRNA splicing, via spliceosome / positive regulation of epithelial cell apoptotic process / FGFR2 alternative splicing / negative regulation of cytokine production / 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 / cytoplasm / cytosol
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsSattler, M. / Wang, I.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1.
Authors: Wang, I. / Hennig, J. / Jagtap, P.K. / Sonntag, M. / Valcarcel, J. / Sattler, M.
History
DepositionJan 13, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleolysin TIA-1 isoform p40


Theoretical massNumber of molelcules
Total (without water)20,5681
Polymers20,5681
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nucleolysin TIA-1 isoform p40 / RNA-binding protein TIA-1 / T-cell-restricted intracellular antigen-1 / TIA-1 / p40-TIA-1


Mass: 20568.096 Da / Num. of mol.: 1 / Fragment: Tandem TIA-1 RRM2 and RRM3 (UNP residues 105-285)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIA1 / Plasmid: pETtrx-1a / Production host: Escherichia coli (E. coli) / References: UniProt: P31483

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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
1332D 1H-13C HSQC
1413D CBCA(CO)NH
1513D HNCO
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1922D 1H-15N HSQC
11013D 1H-13C NOESY
11113D HN(CA)CB
11213D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1-0.7 mM [U-99% 13C; U-99% 15N] TIA-1 RRM2,3, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.1-0.55 mM [U-99% 15N] TIA-1 RRM2,3, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.1-0.5 mM [U-10% 13C] TIA-1 RRM2,3, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMTIA-1 RRM2,3-1[U-99% 13C; U-99% 15N]0.1-0.71
10 mMsodium phosphate-21
50 mMsodium chloride-31
10 mMDTT-41
0.02 %sodium azide-51
mMTIA-1 RRM2,3-6[U-99% 15N]0.1-0.552
10 mMsodium phosphate-72
50 mMsodium chloride-82
10 mMDTT-92
0.02 %sodium azide-102
mMTIA-1 RRM2,3-11[U-10% 13C]0.1-0.53
10 mMsodium phosphate-123
50 mMsodium chloride-133
10 mMDTT-143
0.02 %sodium azide-153
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxchemical shift calculation
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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