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- PDB-6bjh: CIRV p19 mutant T111S in complex with siRNA -

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Basic information

Entry
Database: PDB / ID: 6bjh
TitleCIRV p19 mutant T111S in complex with siRNA
Components
  • RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3')
  • RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3')
  • RNA silencing suppressor p19
KeywordsRNA BINDING PROTEIN / Viral suppressor / RNA silencing siRNA / high affinity for human miRNA-122
Function / homology
Function and homology information


virion component / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense 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 speciesCarnation Italian ringspot virus
Lampyridae (fireflies)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsFoss, D.V. / Schirle, N.T. / MacRae, I.J. / Pezacki, J.P.
Citation
Journal: Febs Open Bio / Year: 2019
Title: Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs.
Authors: Foss, D.V. / Schirle, N.T. / MacRae, I.J. / Pezacki, J.P.
#1: Journal: Biochemistry / Year: 2011
Title: Enhanced specificity of the viral suppressor of RNA silencing protein p19 toward sequestering of human microRNA-122.
Authors: Cheng, J. / Danielson, D.C. / Nasheri, N. / Singaravelu, R. / Pezacki, J.P.
History
DepositionNov 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,0464
Polymers52,0464
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-53 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.788, 46.219, 54.181
Angle α, β, γ (deg.)109.850, 112.110, 95.520
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 19344.348 Da / Num. of mol.: 2 / Mutation: T111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carnation Italian ringspot virus / Gene: ORF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66104
#2: RNA chain RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3')


Mass: 6666.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lampyridae (fireflies)
#3: RNA chain RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3')


Mass: 6690.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lampyridae (fireflies)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 3-12% PEG 1500, 100 mM Sodium Acetate pH 4.6, 10-40 mM MgCl2

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→34.25 Å / Num. obs: 10184 / % possible obs: 85.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.13 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.075 / Rrim(I) all: 0.107 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.58-2.71.80.25110520.4620.2510.35572.5
8.95-34.2520.0252480.9960.0250.03585.5

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RPU

1rpu


Resolution: 2.58→34.037 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.08
RfactorNum. reflection% reflection
Rfree0.278 469 5.12 %
Rwork0.2241 --
obs0.227 9153 77.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.03 Å2 / Biso mean: 32.5888 Å2 / Biso min: 1.33 Å2
Refinement stepCycle: final / Resolution: 2.58→34.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 890 0 129 3300
Biso mean---28.21 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023323
X-RAY DIFFRACTIONf_angle_d0.4294687
X-RAY DIFFRACTIONf_chiral_restr0.03530
X-RAY DIFFRACTIONf_plane_restr0.002455
X-RAY DIFFRACTIONf_dihedral_angle_d8.7421858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5729-2.94510.35861430.29312717286073
2.9451-3.70970.32581460.22442876302276
3.7097-34.04030.22631800.19943091327182
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)
12.4606-0.70411.16253.3137-1.22593.56560.2795-0.1572-0.1520.18250.29840.47250.4482-0.446-0.24560.32070.01470.0420.28380.07990.15622.477149.761376.3665
21.67381.21840.81681.18740.45790.78-0.1005-0.21290.77270.01360.13070.5954-0.488-0.0246-0.00450.92550.17460.12110.463-0.18350.97439.72572.528470.9958
31.3433-0.3218-0.20961.2431-0.49791.47820.1017-0.21530.08120.329-0.1151-0.1151-0.04640.17170.11110.2249-0.03940.0570.1620.1070.08113.851551.552575.1993
40.93230.1496-0.00442.0635-0.97461.49060.0006-0.2422-0.2340.1904-0.1812-0.19830.04990.26250.10860.2518-0.07130.05330.1920.11740.134417.409247.606466.7314
50.16660.01210.27390.0010.01960.4524-0.0040.21110.135-0.1851-0.0019-0.0358-0.1225-0.03950.15260.3954-0.03580.05420.31830.14780.165722.170950.97738.9036
61.6632-0.10210.85080.07490.23991.67790.1227-0.2395-0.34630.11980.17880.14730.3834-0.06680.39240.2819-0.09170.05470.24860.13020.160823.160140.230547.6355
71.7779-0.76250.91811.1999-0.07091.1971-0.0371-0.093-0.2981-0.02690.047-0.0861-0.07980.14080.02670.1466-0.0864-0.09440.26380.04630.333431.487651.993849.8376
80.7220.165-0.24230.20960.3921.2417-0.02170.0290.13190.03020.06620.0302-0.2366-0.17520.0860.13620.0291-0.0710.10160.08260.23717.940755.896653.8378
93.386-0.45811.11781.33230.42060.84560.1148-0.5036-0.13280.32460.0054-0.32730.06410.0098-0.0330.2656-0.1865-0.07020.47490.04510.196627.354352.872660.0597
105.7967-5.80932.81179.2448-0.04623.60780.0337-0.3478-0.7319-0.0351-0.44210.19980.19610.36440.25340.29060.00510.00770.31830.15870.327712.05138.98542.9517
110.6158-0.5737-0.71844.7018-1.8022.3043-0.13650.3704-0.00920.0290.23550.54750.038-0.4058-0.02150.19050.0295-0.04230.23050.00360.45333.924151.71156.081
122.96321.20712.01394.354.07564.17390.6796-0.28540.70431.091-0.40580.8944-1.0697-2.1556-0.19130.82440.11420.41120.68390.1180.8342-6.971467.316462.9078
136.26032.8264-4.79329.5615-4.6324.89880.11530.725-0.5949-0.33570.1740.0120.7204-0.4455-0.29250.3855-0.0056-0.10.2562-0.12590.6511-2.001559.96165.6328
144.0312-1.17292.97653.5355-0.62462.21610.4110.5877-0.4506-0.4726-0.42820.76860.1059-1.1006-0.02320.33440.0689-0.13440.6276-0.05620.37273.222955.247350.2084
151.3830.79541.97480.54351.00893.0054-0.07660.4678-0.4709-0.0690.0428-0.30460.5461-0.0352-0.15660.4846-0.0209-0.07150.3465-0.23640.557710.235334.797746.9169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 38 )A7 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 57 )A39 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 101 )A58 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 147 )A102 - 147
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 38 )B8 - 38
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 74 )B39 - 74
7X-RAY DIFFRACTION7chain 'B' and (resid 75 through 101 )B75 - 101
8X-RAY DIFFRACTION8chain 'B' and (resid 102 through 129 )B102 - 129
9X-RAY DIFFRACTION9chain 'B' and (resid 130 through 149 )B130 - 149
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 5 )C1 - 5
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 15 )C6 - 15
12X-RAY DIFFRACTION12chain 'C' and (resid 16 through 19 )C16 - 19
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 5 )D1 - 5
14X-RAY DIFFRACTION14chain 'D' and (resid 6 through 10 )D6 - 10
15X-RAY DIFFRACTION15chain 'D' and (resid 11 through 20 )D11 - 20

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