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- PDB-6bjv: CIRV p19 protein in complex with siRNA -

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Basic information

Entry
Database: PDB / ID: 6bjv
TitleCIRV p19 protein 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: 2.198 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 7, 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)52,0744
Polymers52,0744
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-55 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.586, 46.997, 54.883
Angle α, β, γ (deg.)109.440, 111.110, 96.780
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: 19358.373 Da / Num. of mol.: 2
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.: 65 / 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: 2.17 Å3/Da / Density % sol: 43.45 %
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: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.198→46.807 Å / Num. obs: 18756 / % possible obs: 93.8 % / Redundancy: 2.2 % / Rpim(I) all: 0.092 / Rrim(I) all: 0.147 / Net I/σ(I): 20.7
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.84 / Num. unique obs: 10 / Rpim(I) all: 0.478 / Rrim(I) all: 0.741 / % possible all: 68.9

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Processing

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

1rpu


Resolution: 2.198→46.807 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 41.52
RfactorNum. reflection% reflection
Rfree0.2971 960 5.12 %
Rwork0.26 --
obs0.262 18756 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 239.75 Å2 / Biso mean: 78.163 Å2 / Biso min: 14.74 Å2
Refinement stepCycle: final / Resolution: 2.198→46.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 890 0 65 3291
Biso mean---52.58 -
Num. residues----336
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)
17.3017-6.7805-0.42786.32530.52344.03120.68080.3706-0.57211.9804-0.0041.848-0.1916-1.46170.18830.82860.05010.12960.3329-0.06980.6438-3.702140.941872.3532
29.6276-5.54157.35184.6907-2.41597.7969-1.9546-1.25120.10764.23360.36820.78640.1139-0.55580.19271.26930.04070.29540.50250.09590.60150.175446.042280.8602
34.4043-4.9678-1.18998.27060.18721.65060.0474-0.021.10630.58980.1288-0.8354-1.0672-0.2161-0.14720.95970.10970.04730.40590.01220.55375.363263.39476.3801
46.59361.70120.43490.44010.12070.06320.88362.02891.63-0.61010.0015-0.1828-1.7890.3662-0.66762.24080.27120.3580.81040.14410.461112.720871.525869.6209
56.03491.02-0.51488.06380.95235.78370.3233-0.223-0.19111.7571-0.3653-0.33960.31240.44030.09390.71430.037-0.0060.39670.01370.336612.688949.982775.6906
68.27182.7106-0.99069.86590.02455.0448-0.2092-0.1097-0.58310.07420.2184-0.657-0.01150.1860.02340.58240.1255-0.01530.4149-0.00950.318915.338545.036166.768
79.24995.6418-6.43744.8435-5.02175.34280.60980.02142.1943-0.19540.078-0.3256-3.09011.5108-0.2481.2762-0.2822-0.02360.63180.17531.022723.956662.015968.4269
85.3416-5.30680.62188.22130.68486.9529-0.5423-0.63421.0788-1.0270.4145-0.1572-1.8271-0.3039-0.43060.92520.0750.10630.4175-0.00350.537711.792355.267438.3013
91.4675-0.1-1.03033.74345.80099.67590.50321.4831-0.156-1.24170.6053-1.3579-1.45950.5283-0.49510.49390.0354-0.00920.7155-0.08310.998322.546851.207836.06
104.8011-0.67241.0061.7213-0.31122.75870.06060.6696-1.18361.53740.1616-1.69890.85740.0469-0.27010.78060.05990.2220.25-0.07010.525224.352737.187243.2258
116.14965.8233-0.95495.5453-0.85490.12450.6973-2.81050.16481.04880.93991.2141.6353-0.2843-0.60961.13170.4348-0.08660.67270.57111.178424.99928.841253.7752
126.1753-5.43471.57274.9834-1.55373.883-0.04560.25790.6892-0.3424-0.1112-0.8022-0.47130.35770.17250.5051-0.01240.12310.2815-0.03670.429125.602250.522448.6708
135.8647-1.7410.59632.21060.35614.9044-0.35-0.07980.22820.41520.53110.5232-0.6551-0.4751-0.03460.5521-0.04150.11840.3433-0.06330.283216.22753.841652.197
143.7656-0.7403-1.01757.83120.11528.466-0.2762-0.55280.68880.14440.3268-1.0058-0.88740.33940.02970.5322-0.08160.02720.3346-0.00480.598122.572953.673658.9189
152.15062.1842-1.5797.28111.85044.9213-0.18320.459-0.19480.5034-0.25830.4656-0.3546-0.39550.42680.85230.02640.15580.4973-0.05340.686710.178537.395442.9316
162.06440.6322-0.24935.71240.8683.840.14150.27920.37170.0655-0.53620.875-0.2425-0.74540.42540.6360.16220.05080.4586-0.13350.63022.083950.489456.4241
178.843-0.0501-7.91420.24160.69449.06341.13751.24611.56121.29820.8089-1.5133-1.6398-1.2357-1.52291.38630.21160.1850.5154-0.16760.9309-8.337866.348667.0055
185.75660.8951-6.65463.91291.52779.42360.17580.1330.1637-0.54970.0869-0.4349-0.4770.199-0.20252.1587-1.1779-0.21792.2191.60133.5618-10.529861.352779.1232
198.2991-4.50051.05543.8411-2.26453.04490.93740.88-0.0455-0.758-0.7943-0.07870.8558-0.53190.01181.08970.17830.08910.6004-0.08480.5754-3.717558.814766.5368
206.4348-2.27010.38765.3999-2.99793.5359-0.02960.34830.5398-0.1301-0.5465-0.35020.1273-0.47420.55730.81270.1073-0.01940.419-0.20260.70844.412646.20952.8425
215.54335.7465-6.39135.9937-7.2019.5199-1.778-0.14760.5865-0.74721.036-0.59713.0434-0.03110.951.13240.0808-0.0760.7358-0.29871.02119.16429.028239.3925
223.55852.057-0.89433.1477-2.92813.188-0.1841-0.0670.37470.85150.39590.3473-2.3487-0.1677-0.57813.908-0.15451.24221.23030.07071.283616.501722.788828.9123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 18 )A2 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 28 )A19 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 47 )A29 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 57 )A48 - 57
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 101 )A58 - 101
6X-RAY DIFFRACTION6chain 'A' and (resid 102 through 144 )A102 - 144
7X-RAY DIFFRACTION7chain 'A' and (resid 145 through 149 )A145 - 149
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 18 )B3 - 18
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 28 )B19 - 28
10X-RAY DIFFRACTION10chain 'B' and (resid 29 through 45 )B29 - 45
11X-RAY DIFFRACTION11chain 'B' and (resid 46 through 58 )B46 - 58
12X-RAY DIFFRACTION12chain 'B' and (resid 59 through 101 )B59 - 101
13X-RAY DIFFRACTION13chain 'B' and (resid 102 through 118 )B102 - 118
14X-RAY DIFFRACTION14chain 'B' and (resid 119 through 148 )B119 - 148
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 5 )C1 - 5
16X-RAY DIFFRACTION16chain 'C' and (resid 6 through 15 )C6 - 15
17X-RAY DIFFRACTION17chain 'C' and (resid 16 through 20 )C16 - 20
18X-RAY DIFFRACTION18chain 'C' and (resid 21 through 21 )C21
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 5 )D1 - 5
20X-RAY DIFFRACTION20chain 'D' and (resid 6 through 15 )D6 - 15
21X-RAY DIFFRACTION21chain 'D' and (resid 16 through 20 )D16 - 20
22X-RAY DIFFRACTION22chain 'D' and (resid 21 through 21 )D21

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