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- PDB-4knq: Crystal structure of 1nt-5'-overhanging double-helical CCG-repeti... -

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Basic information

Entry
Database: PDB / ID: 4knq
TitleCrystal structure of 1nt-5'-overhanging double-helical CCG-repetitive RNA 20mer complexed with RSS p19
Components
  • 5'-R(P*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*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: 1.82 Å
AuthorsTamjar, J. / Katorcha, E. / Popov, A.N. / Malinina, L.
CitationJournal: To be Published
Title: Structural insights into CNG-repetitive RNAs associated with human Trinucleotide Repeat Expansion Diseases (TREDs)
Authors: Tamjar, J. / Katorcha, E. / Cabo, A. / Delgado, S. / Popov, A.N. / Malinina, L.
History
DepositionMay 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
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
B: 5'-R(P*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*G)-3'
A: RNA silencing suppressor p19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1405
Polymers20,8522
Non-polymers2883
Water2,594144
1
B: 5'-R(P*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*CP*GP*CP*G)-3'
A: RNA silencing suppressor p19
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)42,28010
Polymers41,7044
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8540 Å2
ΔGint-128 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.217, 91.217, 147.815
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21A-348-

HOH

31A-411-

HOH

DetailsTHE BIOLOGICAL UNIT IS A P19 HOMODIMER BOUND TO DOUBLE-STRANDED RNA.

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Components

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


Mass: 6338.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA pCCG(CCG)5CG
#2: 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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P69517
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8 M 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: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 21280 / % possible obs: 98.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.139 / Χ2: 1.799 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.82-1.894.40.8519812.919193.6
1.89-1.965.50.64821073.329198.8
1.96-2.055.50.421052.236198.9
2.05-2.165.50.29821201.96199.1
2.16-2.295.50.21321061.706199.2
2.29-2.475.40.18421471.715199.1
2.47-2.725.40.1521301.275199.3
2.72-3.115.30.1321571.195199.6
3.11-3.925.10.12121750.917199.6
3.92-504.80.13322520.9199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2482 / WRfactor Rwork: 0.2155 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8419 / SU B: 5.656 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1153 / SU Rfree: 0.1095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1083 5.1 %RANDOM
Rwork0.1821 ---
obs0.1834 21136 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.76 Å2 / Biso mean: 54.4136 Å2 / Biso min: 23.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å21.08 Å20 Å2
2--1.08 Å2-0 Å2
3----3.49 Å2
Refinement stepCycle: LAST / Resolution: 1.82→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 422 15 144 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0171514
X-RAY DIFFRACTIONr_bond_other_d0.0070.021143
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.7282148
X-RAY DIFFRACTIONr_angle_other_deg1.68332649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.98222.30852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10515174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4671510
X-RAY DIFFRACTIONr_chiral_restr0.1770.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_mcbond_it3.3032.601486
X-RAY DIFFRACTIONr_mcbond_other3.2552.59485
X-RAY DIFFRACTIONr_mcangle_it4.5613.853604
LS refinement shellResolution: 1.82→1.864 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 66 -
Rwork0.346 1303 -
all-1369 -
obs--88.44 %
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)
10.0240.0016-0.06680.01270.01880.8779-0.012-0.031-0.0042-0.0331-0.0340.0121-0.00790.05990.0460.16320.01580.01590.1379-0.00530.143114.123735.390110.9014
20.05980.004-0.05470.0575-0.00120.0520.0831-0.0976-0.0186-0.0302-0.06890.0427-0.11540.0795-0.01430.3336-0.089-0.00480.22080.03610.069726.13847.1891-0.476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 127
2X-RAY DIFFRACTION2B201 - 220

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