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- PDB-1r9f: Crystal structure of p19 complexed with 19-bp small interfering RNA -

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Basic information

Entry
Database: PDB / ID: 1r9f
TitleCrystal structure of p19 complexed with 19-bp small interfering RNA
Components
  • 5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3'
  • 5'-R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'
  • Core protein P19
KeywordsViral protein/RNA / Protein-RNA complex / Dimer / double helix / Viral protein-RNA COMPLEX
Function / homology
Function and homology information


virion component => GO:0044423 / 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 / MAD / Resolution: 1.85 Å
AuthorsYe, K. / Malinina, L. / Patel, D.J.
CitationJournal: Nature / Year: 2003
Title: Recognition of small interfering RNA by a viral suppressor of RNA
Authors: Ye, K. / Malinina, L. / Patel, D.J.
History
DepositionOct 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
B: 5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3'
C: 5'-R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'
A: Core protein P19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3015
Polymers29,1093
Non-polymers1922
Water1,26170
1
B: 5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3'
C: 5'-R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'
A: Core protein P19
hetero molecules

B: 5'-R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3'
C: 5'-R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'
A: Core protein P19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,60210
Polymers58,2186
Non-polymers3844
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
Unit cell
Length a, b, c (Å)91.249, 91.249, 148.630
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
11B-10-

A

DetailsThe biological assemble is a p19 dimer in complex with one siRNA duplex generated from the protein monomer and half RNA (19-bp duplex in half occupancy) in the asymmetric unit by the operation: Y+2/3,X-2/3,-Z+1/3. The 2-fold symmetry operation generates another overlapping half RNA in opposite orientation, compensating the lack of symmetry in RNA duplex itself.

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Components

#1: RNA chain 5'-R(*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 / Details: 5'-OH and 3'-OH
#2: RNA chain 5'-R(*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 / Details: 5'-OH and 3'-OH
#3: Protein Core protein P19


Mass: 15751.966 Da / Num. of mol.: 1 / Fragment: Residues 27-158 / Mutation: L144M, L147M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato bushy stunt virus / Genus: Tombusvirus / Gene: p19 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11690
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.05 Å3/Da / Density % sol: 39.86 %
Crystal growTemperature: 293 K / pH: 7.5
Details: ammonium sulfate, potassium chloride, HEPES-NaOH, dithiothreitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2potassium chloride11
3HEPES-NaOH11
4dithiothreitol11
5H2O11
6ammonium sulfate12
7potassium chloride12
8H2O12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1125000 nMprotein1drop
20.1 M1dropKCl
35 mMHEPES-KOH1drop
410 mM1droppH7.6
51.2-1.6 Mammonium sulfate1reservoir
60.1 MHEPES-NaOH1reservoirpH7.5
71
81

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9791,0.9789,0.9562
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 18, 2003
RadiationMonochromator: DIAMOND (111) DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97891
30.95621
ReflectionResolution: 1.85→50 Å / Num. obs: 39408 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 44.8
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2 / % possible all: 93.2
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 50 Å / Num. obs: 20413 / % possible obs: 99.11 % / Num. measured all: 194486 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 93.2 % / Num. unique obs: 1872 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→14.86 Å / Rfactor Rfree error: 0.005 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1772 4.9 %RANDOM
Rwork0.212 ---
obs0.212 36309 92.3 %-
all-36309 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.85 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.46 Å24.19 Å20 Å2
2--5.46 Å20 Å2
3----10.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.85→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 810 10 70 1862
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 1.86→1.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 220 4.5 %
Rwork0.324 4623 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.3

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