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- PDB-3bs9: X-ray structure of human TIA-1 RRM2 -

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Basic information

Entry
Database: PDB / ID: 3bs9
TitleX-ray structure of human TIA-1 RRM2
ComponentsNucleolysin TIA-1 isoform p40
KeywordsRNA BINDING PROTEIN / RNA Recognition Motif / RRM / RNA binding Domain / RBD / RNA splicing / Apoptosis / Phosphoprotein / RNA-binding
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
IODIDE ION / Cytotoxic granule associated RNA binding protein TIA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKumar, A.O. / Kielkopf, C.L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Structure of the central RNA recognition motif of human TIA-1 at 1.95A resolution.
Authors: Kumar, A.O. / Swenson, M.C. / Benning, M.M. / Kielkopf, C.L.
History
DepositionDec 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleolysin TIA-1 isoform p40
B: Nucleolysin TIA-1 isoform p40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7969
Polymers18,9072
Non-polymers8887
Water2,126118
1
A: Nucleolysin TIA-1 isoform p40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8344
Polymers9,4541
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleolysin TIA-1 isoform p40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9615
Polymers9,4541
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.500, 56.500, 76.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Nucleolysin TIA-1 isoform p40 / RNA-binding protein TIA-1 / p40-TIA-1


Mass: 9453.696 Da / Num. of mol.: 2 / Fragment: RNA recognition motif 2, UNP residues 105-186 / Mutation: E109A, D110A, K112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: P31483
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS THE GLN TO GLU MUTATION REPRESENTS A PROBLEM IN THE DEPOSITED SEQUENCE. ...ACCORDING TO THE AUTHORS THE GLN TO GLU MUTATION REPRESENTS A PROBLEM IN THE DEPOSITED SEQUENCE. THE PDB IS NUMBERED TO MATCH SEQUENCE OF THE ALTERNATIVE ISOFORM P31483-2. HIS94 IN THE PDB FILE CORRESPONDS TO HIS94 IN P31483-2

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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: 1.87 Å3/Da / Density % sol: 34.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1:1 mixture of protein with 15% polyethylene glycol 3350, 0.5 M KI, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER PROTEUM / Detector: CCD / Date: Aug 16, 2006 / Details: Multilayer Graded X-ray Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→24.46 Å / Num. all: 10156 / Num. obs: 10137 / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
CNS1.2refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-terminal RRM of poly-A binding protein, PDB entry 1CVJ

1cvj


Resolution: 1.95→20 Å
RfactorNum. reflection% reflection
Rfree0.2454 9648 -
Rwork0.2156 --
all-10153 -
obs-10137 95 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.299 Å20 Å20 Å2
2--0.299 Å20 Å2
3----0.599 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 7 118 1344

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