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- PDB-5emo: Structure of the star domain of T-STAR in complex with AUUAAA RNA -

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Basic information

Entry
Database: PDB / ID: 5emo
TitleStructure of the star domain of T-STAR in complex with AUUAAA RNA
Components
  • KH domain-containing, RNA-binding, signal transduction-associated protein 3
  • RNA (5'-R(P*AP*UP*UP*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / Protein - RNA complexes STAR protein Alternative splicing KH domain
Function / homology
Function and homology information


PTK6 Regulates Proteins Involved in RNA Processing / regulation of alternative mRNA splicing, via spliceosome / SH3 domain binding / mRNA processing / protein domain specific binding / mRNA binding / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / K Homology domain, type 1 / KH domain / Ribosomal Protein S8; Chain: A, domain 1 ...Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / K Homology domain, type 1 / KH domain / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / KH domain-containing, RNA-binding, signal transduction-associated protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.03 Å
AuthorsDominguez, C. / Feracci, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000526 United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68.
Authors: Feracci, M. / Foot, J.N. / Grellscheid, S.N. / Danilenko, M. / Stehle, R. / Gonchar, O. / Kang, H.S. / Dalgliesh, C. / Meyer, N.H. / Liu, Y. / Lahat, A. / Sattler, M. / Eperon, I.C. / ...Authors: Feracci, M. / Foot, J.N. / Grellscheid, S.N. / Danilenko, M. / Stehle, R. / Gonchar, O. / Kang, H.S. / Dalgliesh, C. / Meyer, N.H. / Liu, Y. / Lahat, A. / Sattler, M. / Eperon, I.C. / Elliott, D.J. / Dominguez, C.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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

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Assembly

Deposited unit
A: KH domain-containing, RNA-binding, signal transduction-associated protein 3
B: KH domain-containing, RNA-binding, signal transduction-associated protein 3
E: RNA (5'-R(P*AP*UP*UP*AP*AP*A)-3')
F: RNA (5'-R(P*AP*UP*UP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)46,0814
Polymers46,0814
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-28 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.601, 79.967, 53.831
Angle α, β, γ (deg.)90.000, 101.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KH domain-containing, RNA-binding, signal transduction-associated protein 3 / RNA-binding protein T-Star / Sam68-like mammalian protein 2 / SLM-2 / Sam68-like phosphotyrosine protein


Mass: 21156.258 Da / Num. of mol.: 2 / Fragment: RNA binding protein
Source method: isolated from a genetically manipulated source
Details: N-terminus GA residues from tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: KHDRBS3, SALP, SLM2 / Plasmid: pLEICS 03 / Production host: Escherichia coli (E. coli) / References: UniProt: O75525
#2: RNA chain RNA (5'-R(P*AP*UP*UP*AP*AP*A)-3')


Mass: 1884.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaCl, Na-HEPES, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.03→28.51 Å / Num. obs: 7908 / % possible obs: 94.8 % / Redundancy: 2.6 % / Biso Wilson estimate: 55.46 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.081 / Net I/σ(I): 8.1 / Num. measured all: 20367
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.03-3.112.60.4821.913955470.8040.34390.3
13.54-28.512.80.02833.6196710.9970.02178.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EL3

5el3


Resolution: 3.03→28.508 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 787 9.98 %RAMDOM
Rwork0.2208 7100 --
obs0.2256 7887 93.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.05 Å2 / Biso mean: 55.8537 Å2 / Biso min: 15.42 Å2
Refinement stepCycle: final / Resolution: 3.03→28.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 256 0 0 2606
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032679
X-RAY DIFFRACTIONf_angle_d0.6693647
X-RAY DIFFRACTIONf_chiral_restr0.043411
X-RAY DIFFRACTIONf_plane_restr0.006424
X-RAY DIFFRACTIONf_dihedral_angle_d13.5641632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0301-3.21970.34521300.2811178130894
3.2197-3.46790.34891320.2631198133095
3.4679-3.81610.27561330.23891193132695
3.8161-4.36660.26071310.20481176130793
4.3666-5.4950.25711350.20041189132494
5.495-28.50960.21881260.19971166129290

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