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- PDB-5elr: Structure of the KH-QUA2 domain of T-STAR in complex with AAUAAU RNA -

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Basic information

Entry
Database: PDB / ID: 5elr
TitleStructure of the KH-QUA2 domain of T-STAR in complex with AAUAAU RNA
Components
  • KH domain-containing, RNA-binding, signal transduction-associated protein 3
  • RNA (5'-R(*AP*AP*UP*AP*AP*U)-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 / mRNA processing / SH3 domain binding / 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 / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
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 / Resolution: 2.3 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 5, 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 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA (5'-R(*AP*AP*UP*AP*AP*U)-3')
C: KH domain-containing, RNA-binding, signal transduction-associated protein 3
D: KH domain-containing, RNA-binding, signal transduction-associated protein 3


Theoretical massNumber of molelcules
Total (without water)32,6743
Polymers32,6743
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-14 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.380, 45.560, 151.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 50 - 157 / Label seq-ID: 3 - 110

Dom-IDAuth asym-IDLabel asym-ID
1CB
2DC

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Components

#1: RNA chain RNA (5'-R(*AP*AP*UP*AP*AP*U)-3')


Mass: 1884.197 Da / Num. of mol.: 1 / Fragment: RNA binding protein / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein KH domain-containing, RNA-binding, signal transduction-associated protein 3 / T-STAR KH - QUA2 / RNA-binding protein T-Star / Sam68-like mammalian protein 2 / SLM-2 / Sam68-like ...T-STAR KH - QUA2 / RNA-binding protein T-Star / Sam68-like mammalian protein 2 / SLM-2 / Sam68-like phosphotyrosine protein


Mass: 15394.745 Da / Num. of mol.: 2 / Fragment: UNP residues 50-183
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 / Production host: Escherichia coli (E. coli) / References: UniProt: O75525
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Imidazole, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionRedundancy: 12.6 % / Number: 173881 / Rmerge(I) obs: 0.081 / D res high: 2.3 Å / D res low: 45.56 Å / Num. obs: 13783 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.32.3610.92112.8
10.2945.5610.0538.6
ReflectionResolution: 2.3→45.56 Å / Num. obs: 13783 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Net I/σ(I): 21.2 / Num. measured all: 173881
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3612.80.9213.2127489950.8690.267100
10.29-45.568.60.05343.516931980.9970.01999.1

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Processing

Software
NameVersionClassification
Aimless0.2.12data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.68 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2636 / WRfactor Rwork: 0.2228 / FOM work R set: 0.7981 / SU B: 15.715 / SU ML: 0.187 / SU R Cruickshank DPI: 0.3197 / SU Rfree: 0.2423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 687 5 %RANDOM
Rwork0.2273 ---
obs0.2294 13046 99.96 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 149.78 Å2 / Biso mean: 56.893 Å2 / Biso min: 27.47 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å20 Å2
2--2.68 Å2-0 Å2
3----5.65 Å2
Refinement stepCycle: final / Resolution: 2.3→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 106 0 21 1927
Biso mean---47.48 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191951
X-RAY DIFFRACTIONr_bond_other_d0.0060.021923
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9512630
X-RAY DIFFRACTIONr_angle_other_deg1.45434459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71524.62580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90815375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3281510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212062
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02413
X-RAY DIFFRACTIONr_mcbond_it3.4412.682898
X-RAY DIFFRACTIONr_mcbond_other3.4432.682897
X-RAY DIFFRACTIONr_mcangle_it4.6224.0161119
Refine LS restraints NCS

Ens-ID: 1 / Number: 25560 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1C
2D
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 54 -
Rwork0.333 937 -
all-991 -
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)
12.3237-0.7637-1.3422.41841.1636.8105-0.1605-0.1841-0.20740.15280.1431-0.00240.6375-0.24890.01740.0679-0.030.00080.06590.02050.32910.9322.486-10.166
24.05950.8848-1.33022.4232-1.09853.78330.21250.1770.04020.0473-0.2096-0.2172-0.15140.1685-0.00290.0932-0.0350.00990.06250.00740.379531.17617.146-29.738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C48 - 158
2X-RAY DIFFRACTION2D50 - 163

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