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- PDB-5o3j: Crystal structure of TIA-1 RRM2 in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 5o3j
TitleCrystal structure of TIA-1 RRM2 in complex with RNA
Components
  • Nucleolysin TIA-1 isoform p40
  • RNA (5'-R(P*UP*UP*C)-3')
KeywordsRNA BINDING PROTEIN / TIA-1 / RRM
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 / 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
Similarity search - Domain/homology
RNA / Cytotoxic granule associated RNA binding protein TIA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsSonntag, M. / Jagtap, P.K.A. / Hennig, J. / Sattler, M.
CitationJournal: Angew Chem Int Ed Engl / Year: 2017
Title: Segmental, Domain-Selective Perdeuteration and Small-Angle Neutron Scattering for Structural Analysis of Multi-Domain Proteins.
Authors: Miriam Sonntag / Pravin Kumar Ankush Jagtap / Bernd Simon / Marie-Sousai Appavou / Arie Geerlof / Ralf Stehle / Frank Gabel / Janosch Hennig / Michael Sattler /
Abstract: Multi-domain proteins play critical roles in fine-tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers ...Multi-domain proteins play critical roles in fine-tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic rearrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi-domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA-1 using Sortase A mediated protein ligation. We show that domain-selective perdeuteration combined with contrast-matched small-angle neutron scattering (SANS), SAXS and computational modeling provides valuable information to precisely define relative domain arrangements. The approach is generally applicable to study conformational arrangements of individual domains in multi-domain proteins and changes induced by ligand binding.
History
DepositionMay 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: RNA (5'-R(P*UP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)9,7622
Polymers9,7622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.310, 44.310, 85.720
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: 8888.953 Da / Num. of mol.: 1 / Fragment: RRM2 domain, UNP Residues 93-170
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: RNA chain RNA (5'-R(P*UP*UP*C)-3')


Mass: 872.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 50mM MES pH6, 5mM MgSO4, 5% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.97→35.02 Å / Num. obs: 1980 / % possible obs: 98 % / Redundancy: 7.8 % / CC1/2: 0.93 / Rmerge(I) obs: 0.0867 / Net I/σ(I): 15.34

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BS9

3bs9


Resolution: 2.97→35.02 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.909 / SU B: 31.878 / SU ML: 0.526 / Cross valid method: THROUGHOUT / ESU R Free: 0.557 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3116 98 5 %RANDOM
Rwork0.25095 ---
obs0.25387 1859 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 84.381 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å21.16 Å20 Å2
2--2.32 Å2-0 Å2
3----7.52 Å2
Refinement stepCycle: 1 / Resolution: 2.97→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms600 43 0 0 643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019663
X-RAY DIFFRACTIONr_bond_other_d0.0010.02551
X-RAY DIFFRACTIONr_angle_refined_deg0.9061.834906
X-RAY DIFFRACTIONr_angle_other_deg0.83731253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.452579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78723.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7931579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.869154
X-RAY DIFFRACTIONr_chiral_restr0.0620.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02176
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4838.832319
X-RAY DIFFRACTIONr_mcbond_other1.4838.838318
X-RAY DIFFRACTIONr_mcangle_it2.64113.248397
X-RAY DIFFRACTIONr_mcangle_other2.63813.24398
X-RAY DIFFRACTIONr_scbond_it0.929.093344
X-RAY DIFFRACTIONr_scbond_other0.9119.078341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.70113.634509
X-RAY DIFFRACTIONr_long_range_B_refined3.956715
X-RAY DIFFRACTIONr_long_range_B_other3.959714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.967→3.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 6 -
Rwork0.31 126 -
obs--96.35 %

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