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- PDB-6bjg: CIRV p19 mutant T111H in complex with siRNA -

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Basic information

Entry
Database: PDB / ID: 6bjg
TitleCIRV p19 mutant T111H 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 binding protein p19 / altered affinity for microRNA
Function / homology
Function and homology information


virion component / 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: 2.29 Å
AuthorsFoss, D.V. / Schirle, N. / Pezacki, J.P. / Macrae, I.J.
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)52,1484
Polymers52,1484
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-53 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.386, 46.934, 54.623
Angle α, β, γ (deg.)109.330, 111.120, 96.610
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: 19395.416 Da / Num. of mol.: 2 / Mutation: T111H
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 / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
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: 2.29→34.94 Å / Num. obs: 15496 / % possible obs: 87.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 31.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.031 / Rrim(I) all: 0.062 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.29-2.383.70.14513680.9770.0860.16978.2
8.89-34.943.90.0282720.9980.0160.03288.9

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RPU

1rpu


Resolution: 2.29→34.826 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.83
RfactorNum. reflection% reflection
Rfree0.2574 794 5.14 %
Rwork0.2122 --
obs0.2146 15444 87.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.6 Å2 / Biso mean: 45.0256 Å2 / Biso min: 12.88 Å2
Refinement stepCycle: final / Resolution: 2.29→34.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 890 0 121 3318
Biso mean---35.92 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043351
X-RAY DIFFRACTIONf_angle_d0.5594723
X-RAY DIFFRACTIONf_chiral_restr0.031532
X-RAY DIFFRACTIONf_plane_restr0.003459
X-RAY DIFFRACTIONf_dihedral_angle_d11.2991360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.29-2.43160.33141280.2674232384
2.4316-2.61930.31731120.2608242185
2.6193-2.88270.31021300.262252290
2.8827-3.29960.30211360.2253238486
3.2996-4.15610.21461460.1831254992
4.1561-34.8260.2271420.186245188
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)
18.44771.49660.5423.4858-1.33815.48861.45490.9561-1.5031-0.1643-0.52630.3126-0.3159-0.87280.34510.3339-0.06030.32110.26120.21860.3036-0.216244.130471.955
23.3067-2.87832.74335.6783-5.12826.6508-0.3623-0.969-0.2850.0737-0.10840.54920.2621-1.3333-0.11440.5477-0.09120.16590.47760.00750.23872.207553.12278.6339
32.4882-0.94680.39985.3686-0.07120.20720.323-0.61380.27571.1815-0.06550.1779-0.0747-0.2305-0.26160.57620.01780.12870.3142-0.01780.21647.27354.733278.7517
43.1683-3.822-0.38687.02360.91223.85230.88580.48112.52560.2398-0.0447-0.6594-0.79870.4573-0.76130.6381-0.0940.11670.46970.02370.799811.295272.80572.6715
53.00410.21720.9475.6644-0.29054.9755-0.137-0.04310.17430.1946-0.07080.1494-0.20170.27560.18410.3066-0.02070.10530.15590.03240.097313.00254.450672.8322
62.0868-2.2989-2.06833.42430.76064.82870.236-0.77420.53340.6772-0.1171-0.8421-0.67480.3950.00810.4542-0.0585-0.26630.2617-0.03150.24821.897955.04579.1984
73.11622.6724-0.39723.3710.87221.2823-0.2013-0.0713-0.79780.24530.0347-0.43540.86060.6495-0.03070.68380.02680.09420.21520.03220.391112.158636.641572.9667
84.80842.26640.70583.03222.07434.982-0.09510.11220.6334-0.3366-0.02030.8467-0.4125-0.11520.05350.1670.08180.07280.1505-0.00260.122415.835754.557966.0712
95.22561.7093-0.28076.53530.4835.5007-0.2478-0.181-0.36160.47980.2051-1.26050.38460.67240.03160.2061-0.037-0.03780.30520.01150.255522.186548.126566.9687
102.81511.5739-2.32154.4003-2.50753.48140.52470.89490.4155-1.8823-0.245-0.008-0.853-0.4416-0.22430.82090.01990.1350.21070.09640.221218.536252.412436.4334
113.69830.64430.42983.83610.96153.1465-0.20070.0008-0.6499-0.6165-0.0502-1.40130.65350.27350.12840.30840.01980.14630.22640.03740.34627.059738.059845.6081
122.6578-0.2383-0.2194.2823-0.71263.1487-0.00730.0386-0.1443-0.074-0.0697-0.60360.01790.23940.05890.159-0.04730.08720.16610.00320.256328.899748.430849.4512
133.095-0.0449-0.25792.44450.47043.86480.0634-0.12380.36160.13130.0322-0.5816-0.80.1726-0.01410.2448-0.08230.05640.1544-0.00570.258623.781856.104554.5655
146.87322.9695-0.46247.2562-0.29918.2977-0.02360.1880.39480.0209-0.32830.3669-0.6508-0.20680.32790.39480.0147-0.0270.1793-0.01980.252413.103438.58642.7834
153.81860.8045-0.87315.3388-1.21625.86420.03240.4642-1.0964-0.11180.1492-0.8567-0.0362-1.1372-0.20480.2062-0.0192-0.01120.4302-0.03130.54172.751942.589555.8161
164.49952.2763-1.31513.9108-0.39114.78251.31060.32970.5267-0.0944-0.77251.1697-1.2358-1.1697-0.31930.56590.18620.02570.4697-0.02090.60791.371863.942259.9801
173.63094.13143.42777.22995.49815.4603-0.2669-0.17520.5129-1.243-0.26110.9585-0.9075-0.6670.4250.65250.05170.10690.30240.02310.4045-0.710460.443666.5224
184.0019-5.318-0.8188.21243.60277.5494-0.65780.95230.9364-0.1433-0.4035-0.96830.3417-1.66330.83370.5064-0.01420.02490.42710.05580.60263.706855.522150.6633
195.233-0.3573-0.13756.33070.1789.40620.22130.24290.138-0.517-0.59550.66940.8351-0.40380.31050.26640.0299-0.04390.2573-0.05710.478210.496835.134348.7575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 17 )A6 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 22 )A18 - 22
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 40 )A23 - 40
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 57 )A41 - 57
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 79 )A58 - 79
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 91 )A80 - 91
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 108 )A92 - 108
8X-RAY DIFFRACTION8chain 'A' and (resid 109 through 118 )A109 - 118
9X-RAY DIFFRACTION9chain 'A' and (resid 119 through 147 )A119 - 147
10X-RAY DIFFRACTION10chain 'B' and (resid 8 through 24 )B8 - 24
11X-RAY DIFFRACTION11chain 'B' and (resid 25 through 57 )B25 - 57
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 91 )B58 - 91
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 149 )B92 - 149
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 5 )C1 - 5
15X-RAY DIFFRACTION15chain 'C' and (resid 6 through 10 )C6 - 10
16X-RAY DIFFRACTION16chain 'C' and (resid 11 through 19 )C11 - 19
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 5 )D1 - 5
18X-RAY DIFFRACTION18chain 'D' and (resid 6 through 10 )D6 - 10
19X-RAY DIFFRACTION19chain 'D' and (resid 11 through 19 )D11 - 19

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