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- PDB-4j39: Crystal structure of p19 in complex with double-helical 19mer RNA... -

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Basic information

Entry
Database: PDB / ID: 4j39
TitleCrystal structure of p19 in complex with double-helical 19mer RNA p(CAG)3C(CUG)3
Components
  • 5'-R(P*CP*AP*GP*CP*AP*GP*CP*AP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
  • RNA silencing suppressor p19
KeywordsRNA BINDING PROTEIN/RNA / RNA silencing suppression / trinucleotide repeats / dimer / RNA BINDING PROTEIN-RNA complex
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 speciesTomato bushy stunt virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTamjar, 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
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: 5'-R(P*CP*AP*GP*CP*AP*GP*CP*AP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9666
Polymers20,5822
Non-polymers3844
Water2,720151
1
A: RNA silencing suppressor p19
B: 5'-R(P*CP*AP*GP*CP*AP*GP*CP*AP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
hetero molecules

A: RNA silencing suppressor p19
B: 5'-R(P*CP*AP*GP*CP*AP*GP*CP*AP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,93212
Polymers41,1644
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8510 Å2
ΔGint-153 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.611, 90.611, 148.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21A-365-

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 / Production host: Escherichia coli (E. coli) / References: UniProt: P69517
#2: RNA chain 5'-R(P*CP*AP*GP*CP*AP*GP*CP*AP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*G)-3'


Mass: 6068.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA p(CAG)3C(CUG)3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.3 mM ammonium sulfate, 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 25529 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.286 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20695 1255 4.9 %RANDOM
Rwork0.18048 ---
obs0.18175 24226 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.088 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å21.39 Å20 Å2
2--2.77 Å20 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 405 20 151 1566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211521
X-RAY DIFFRACTIONr_bond_other_d0.0010.02903
X-RAY DIFFRACTIONr_angle_refined_deg2.4792.3062154
X-RAY DIFFRACTIONr_angle_other_deg2.59532205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42722.40754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34715181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3731511
X-RAY DIFFRACTIONr_chiral_restr0.2180.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3890.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.811.5607
X-RAY DIFFRACTIONr_mcbond_other0.5351.5248
X-RAY DIFFRACTIONr_mcangle_it3.0032982
X-RAY DIFFRACTIONr_scbond_it3.2613914
X-RAY DIFFRACTIONr_scangle_it4.5434.51172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 101 -
Rwork0.295 1604 -
obs--90.98 %

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