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- PDB-4jk0: Crystal structure of T89Q-mutant of RNA silencing suppressor p19 ... -

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Basic information

Entry
Database: PDB / ID: 4jk0
TitleCrystal structure of T89Q-mutant of RNA silencing suppressor p19 with 2nt-5'-overhanging double-helical RNA 21mer pUUUG(CUG)5CU
Components
  • 5'-R(P*UP*UP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U)-3'
  • RNA silencing suppressor p19
KeywordsRNA BINDING PROTEIN/RNA / RNA silencing suppression / trinucleotide repeats / protein-RNA complex / dimer / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


virion component / symbiont-mediated suppression of host innate immune response / RNA binding
Similarity search - Function
RNA silencing suppressor P19 / Tombusvirus p19 core protein / Tombusvirus P19 superfamily / Tombusvirus P19 core protein / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA silencing suppressor p19
Similarity search - Component
Biological speciesTomato bushy stunt virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKatorcha, E. / Tamjar, J. / Popov, A.N. / Malinina, L.
CitationJournal: To be Published
Title: Procrustean bed of RNA silencing suppression
Authors: Katorcha, E. / Tamjar, J. / Popov, A.N. / Malinina, L.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RNA silencing suppressor p19
B: 5'-R(P*UP*UP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3454
Polymers21,1532
Non-polymers1922
Water3,369187
1
D: RNA silencing suppressor p19
B: 5'-R(P*UP*UP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U)-3'
hetero molecules

D: RNA silencing suppressor p19
B: 5'-R(P*UP*UP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6908
Polymers42,3064
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8920 Å2
ΔGint-128 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.391, 90.391, 148.909
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11D-272-

HOH

21D-308-

HOH

31B-719-

HOH

DetailsTHE BIOLOGICAL UNIT IS A P19 HOMODIMER BOUND TO DOUBLE-STRANDED RNA.

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Components

#1: Protein RNA silencing suppressor p19 / 19 kDa symptom severity modulator


Mass: 14540.231 Da / Num. of mol.: 1 / Fragment: UNP residues 27-149 / Mutation: T111Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato bushy stunt virus / Gene: ORF4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P69517
#2: RNA chain 5'-R(P*UP*UP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U)-3'


Mass: 6612.860 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA pUUUG(CUG)5CU
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6 M ammonium sulfate, 0.1 M citric acid, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 10511 / % possible obs: 98.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.118 / Χ2: 1.124 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.382.70.6310211.231198.5
2.38-2.482.70.49110381.176198.8
2.48-2.592.70.3810401.126199
2.59-2.732.70.3210431.147199
2.73-2.92.70.23310551.112199.3
2.9-3.122.70.15810571.118199.2
3.12-3.432.70.09810461.061199.4
3.43-3.932.70.07910580.977199.2
3.93-4.952.70.08610771.183199.3
4.95-302.70.06410761.109194.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R9F

1r9f


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.1892 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8256 / SU B: 13.512 / SU ML: 0.171 / SU R Cruickshank DPI: 0.2907 / SU Rfree: 0.2316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 505 4.8 %RANDOM
Rwork0.1836 ---
obs0.1867 10506 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 273.72 Å2 / Biso mean: 43.1562 Å2 / Biso min: 17.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.9 Å20 Å2
2--0.9 Å2-0 Å2
3----2.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 439 10 187 1612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0171497
X-RAY DIFFRACTIONr_bond_other_d0.0040.021123
X-RAY DIFFRACTIONr_angle_refined_deg1.551.7132120
X-RAY DIFFRACTIONr_angle_other_deg0.9932609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6455118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6522250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.811510
X-RAY DIFFRACTIONr_chiral_restr0.090.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_mcbond_it2.0422.822477
X-RAY DIFFRACTIONr_mcbond_other2.0412.822477
X-RAY DIFFRACTIONr_mcangle_it3.164.205593
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 43 -
Rwork0.226 696 -
all-739 -
obs--98.27 %
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)
10.4755-0.13760.24710.5550.0731.1002-0.0123-0.0132-0.0114-0.0097-0.0197-0.02340.0041-0.01970.0320.01120.00040.01030.0127-0.00310.012423.442929.4168-10.8632
20.1590.0336-0.1460.43580.21450.29810.0327-0.05060.02990.0063-0.0250.0649-0.07140.0879-0.00770.0708-0.04680.00430.092-0.00820.01426.558245.1048-0.1984
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D3 - 127
2X-RAY DIFFRACTION2B501 - 521

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