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- PDB-5ith: TIA-1 RRM2 recognition of target oligonucleotide -

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Basic information

Entry
Database: PDB / ID: 5ith
TitleTIA-1 RRM2 recognition of target oligonucleotide
Components
  • DNA (5'-D(*AP*CP*TP*CP*C*TP*TP*TP*TP*T)-3')
  • Nucleolysin TIA-1 isoform p40
Keywordsrna binding protein/dna / RRM / RNA/DNA binding domain / Poly U binding preference / aromatic base stacking interactions / DNA binding protein-DNA complex / rna binding protein-dna complex
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 / cytosol / cytoplasm
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
DNA / Cytotoxic granule associated RNA binding protein TIA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsWaris, S. / Wilce, J.A. / Wilce, M.C.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: TIA-1 RRM23 binding and recognition of target oligonucleotides.
Authors: Waris, S. / Garcia-Maurino, S.M. / Sivakumaran, A. / Beckham, S.A. / Loughlin, F.E. / Gorospe, M. / Diaz-Moreno, I. / Wilce, M.C.J. / Wilce, J.A.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleolysin TIA-1 isoform p40
B: DNA (5'-D(*AP*CP*TP*CP*C*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)13,2092
Polymers13,2092
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-5 kcal/mol
Surface area5030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.430, 45.430, 84.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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: 10248.503 Da / Num. of mol.: 1 / Fragment: unp residues 93-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31483
#2: DNA chain DNA (5'-D(*AP*CP*TP*CP*C*TP*TP*TP*TP*T)-3')


Mass: 2960.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 1500, Malonate-Imidazole-Borate, pH 8 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.7108 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7108 Å / Relative weight: 1
ReflectionResolution: 2.31→22.974 Å / Num. obs: 4381 / % possible obs: 100 % / Redundancy: 12.6 % / Rsym value: 0.045 / Net I/σ(I): 35.07
Reflection shellResolution: 2.31→2.393 Å / Mean I/σ(I) obs: 5.17 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHENIXphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BS9

3bs9


Resolution: 2.31→22.974 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 218 4.98 %
Rwork0.2277 --
obs0.2293 4374 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→22.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 55 0 5 681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005698
X-RAY DIFFRACTIONf_angle_d0.908951
X-RAY DIFFRACTIONf_dihedral_angle_d18.019242
X-RAY DIFFRACTIONf_chiral_restr0.03496
X-RAY DIFFRACTIONf_plane_restr0.004115
LS refinement shellResolution: 2.3101→2.9095 Å
RfactorNum. reflection% reflection
Rfree0.3509 108 -
Rwork0.3179 2066 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.18430.4585-1.06976.77780.15165.28640.2981-0.1318-0.0923-0.07190.0762-0.40442.16791.9811-0.21190.6130.3841-0.01670.8431-0.10640.4372-0.6848-19.1692-1.7093
28.22484.83471.0945.46572.04616.05070.4508-1.08622.0217-0.2886-0.2517-1.3442-1.85710.8532-0.28740.4511-0.1710.00041.3833-0.22150.91795.4776-6.27832.8541
35.4809-0.0574-0.26297.8012-0.74843.49860.21630.0539-0.4458-0.2610.11741.11021.25540.0954-0.23710.62850.0805-0.05970.4517-0.0020.5376-8.0912-20.89110.6705
44.25030.43170.92497.0471-0.91154.7131-0.5387-0.70992.268-1.39950.0222-0.45010.31310.8454-0.32720.89760.14710.17320.5604-0.01841.0878-5.2889-7.3255-0.4834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 93 through 126 )
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 171 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 3 )

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