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- PDB-1rpu: Crystal Structure of CIRV p19 bound to siRNA -

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Basic information

Entry
Database: PDB / ID: 1rpu
TitleCrystal Structure of CIRV p19 bound to siRNA
Components
  • 19 kDa protein
  • 5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*UP*CP*AP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'
KeywordsRNA Binding Protein/RNA / RNAi / PROTEIN-RNA COMPLEX / RNA DOUBLE HELIX / RNA LENGTH RECOGNITION / 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 speciesCarnation Italian ringspot virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsVargason, J.M. / Szittya, G. / Burgyan, J. / Hall, T.M.T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Size selective recognition of siRNA by an RNA silencing suppressor
Authors: Vargason, J.M. / Szittya, G. / Burgyan, J. / Hall, T.M.T.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*UP*CP*AP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'
D: 5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*UP*CP*AP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'
A: 19 kDa protein
B: 19 kDa protein


Theoretical massNumber of molelcules
Total (without water)52,0794
Polymers52,0794
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.400, 115.400, 128.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain 5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*UP*CP*AP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'


Mass: 6680.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by Dharmacon
#2: Protein 19 kDa protein


Mass: 19358.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carnation Italian ringspot virus / Genus: Tombusvirus / Gene: p19 / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q66104
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG MME 2000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG MME 200011
2ammonium sulfate11
3sodium acetate11
4H2O11
5PEG MME 200012
6ammonium sulfate12
7sodium acetate12
8H2O12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122.5 %(w/v)PEG2000 MME1reservoir
2100 mMsodium acetate1reservoirpH4.6
3200 mMammonium sulfate1reservoir
41
51
61
71
81

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 17767 / Num. obs: 17767 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.087
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.381 / % possible all: 95.4
Reflection
*PLUS
% possible obs: 98.8 % / Redundancy: 18.9 % / Num. measured all: 318939 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 95.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.289 862 RANDOM
Rwork0.224 --
all0.24 17767 -
obs0.24 17767 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 1780 0 111 4055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.18
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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