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- PDB-4jgn: Crystal structure of RNA silencing suppressor p19 with 1nt-5'-ove... -

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Basic information

Entry
Database: PDB / ID: 4jgn
TitleCrystal structure of RNA silencing suppressor p19 with 1nt-5'-overhanging double-helical RNA 20mer pUUG(CUG)5CU
Components
  • 5'-R(P*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: 1.86 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 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 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 / pdbx_struct_special_symmetry / 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
A: RNA silencing suppressor p19
E: 5'-R(P*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)21,0124
Polymers20,8202
Non-polymers1922
Water2,378132
1
A: RNA silencing suppressor p19
E: 5'-R(P*UP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U)-3'
hetero molecules

A: RNA silencing suppressor p19
E: 5'-R(P*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)42,0248
Polymers41,6404
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8360 Å2
ΔGint-122 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.362, 89.362, 147.936
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
11A-452-

HOH

21A-458-

HOH

31A-463-

HOH

41E-602-

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: 14513.208 Da / Num. of mol.: 1 / Fragment: UNP residues 27-149
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*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*U)-3'


Mass: 6306.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA pUUG(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.: 132 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8 M ammonium sulfate, 0.1 M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 19385 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.082 / Χ2: 1.524 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.86-1.934.30.64419011.909199.9
1.93-24.90.38719201.5981100
2-2.094.90.27519181.5661100
2.09-2.214.90.19819071.5151100
2.21-2.344.90.15719401.5681100
2.34-2.524.90.13219191.531199.9
2.52-2.784.90.10319391.52199.8
2.78-3.184.90.08619431.528199.7
3.18-4.014.80.06919581.432199.6
4.01-504.60.0620401.126199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R9F

1r9f


Resolution: 1.86→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2363 / WRfactor Rwork: 0.1965 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8603 / SU B: 5.886 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1262 / SU Rfree: 0.1173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 997 5.2 %RANDOM
Rwork0.1834 ---
obs0.1848 19254 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.87 Å2 / Biso mean: 40.4587 Å2 / Biso min: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20.86 Å20 Å2
2--1.72 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 1.86→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 419 10 132 1575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211514
X-RAY DIFFRACTIONr_angle_refined_deg2.4412.2932142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82922.45353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44515171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0451510
X-RAY DIFFRACTIONr_chiral_restr0.1750.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211012
X-RAY DIFFRACTIONr_mcbond_it1.6271.5620
X-RAY DIFFRACTIONr_mcangle_it3.0452997
X-RAY DIFFRACTIONr_scbond_it3.6093894
X-RAY DIFFRACTIONr_scangle_it5.2924.51145
LS refinement shellResolution: 1.86→1.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 84 -
Rwork0.301 1286 -
all-1370 -
obs--99.42 %
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)
10.6621-0.11820.20930.5889-0.31231.8011-0.0149-0.0175-0.0017-0.002-0.0249-0.01680.02370.04380.03980.01230.00080.01810.005-0.00160.030413.968834.325111.2705
20.3612-0.02740.10610.2533-0.07350.2537-0.01880.01710.05490.0099-0.0113-0.0454-0.15260.09690.03010.1301-0.02070.01120.11150.00440.116925.370945.9263-0.3378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 127
2X-RAY DIFFRACTION2E502 - 521

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