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- PDB-4kq0: Crystal structure of double-helical CGG-repetitive RNA 19mer comp... -

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Basic information

Entry
Database: PDB / ID: 4kq0
TitleCrystal structure of double-helical CGG-repetitive RNA 19mer complexed with RSS p19
Components
  • 5'-R(P*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*C)-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: 2.1 Å
AuthorsCabo, A. / Katorcha, E. / Tamjar, J. / 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 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*C)-3'
D: RNA silencing suppressor p19
E: 5'-R(P*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,85810
Polymers43,2824
Non-polymers5766
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-137 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.926, 90.926, 147.791
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

21A-469-

HOH

31A-495-

HOH

41D-458-

HOH

51D-475-

HOH

61D-501-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13A
23B
33D
43E
14B
24E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 127
2111D2 - 127
1121B1 - 9
2121E1 - 9
1131A301 - 515
2131B101 - 119
3131D301 - 515
4131E101 - 118
1141B11 - 19
2141E11 - 19

NCS ensembles :
ID
1
2
3
4
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: 15407.189 Da / Num. of mol.: 2 / Fragment: UNP residues 27-158 / Mutation: L144M (L122M), L147M (L125M)
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
#2: RNA chain 5'-R(P*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*GP*GP*CP*C)-3'


Mass: 6233.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: siRNA pGG(CGG)5CC
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7 M ammonium sulfate, 0.1 M HEPES, 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: 0.9834 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: 0.9834 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 13256 / % possible obs: 94.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.061 / Χ2: 0.963 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.182.80.2939710.917169.8
2.18-2.262.90.21612390.931190.3
2.26-2.373.20.20313520.978197.8
2.37-2.493.20.1513711.049198.1
2.49-2.653.20.11613540.929198.3
2.65-2.853.20.08913820.991198.6
2.85-3.143.20.06413910.897198.6
3.14-3.593.20.04913720.94198.8
3.59-4.523.20.05513961198.3
4.52-403.10.05114280.97196.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2591 / WRfactor Rwork: 0.2041 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8407 / SU B: 4.389 / SU ML: 0.119 / SU R Cruickshank DPI: 0.2014 / SU Rfree: 0.1771 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1263 5 %RANDOM
Rwork0.1795 ---
obs0.1818 24052 94.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.34 Å2 / Biso mean: 48.8329 Å2 / Biso min: 23.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å21.18 Å2-0 Å2
2--1.18 Å20 Å2
3----3.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 834 30 267 3101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0172980
X-RAY DIFFRACTIONr_bond_other_d0.0020.022226
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.7054224
X-RAY DIFFRACTIONr_angle_other_deg1.02235148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17822.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18415336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1571520
X-RAY DIFFRACTIONr_chiral_restr0.1060.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
X-RAY DIFFRACTIONr_mcbond_it3.9493.876972
X-RAY DIFFRACTIONr_mcbond_other3.9313.87971
X-RAY DIFFRACTIONr_mcangle_it5.1845.7651208
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A19090.2
2B2890.28
3A1480.38
4B2850.32
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 70 -
Rwork0.23 1252 -
all-1322 -
obs--67.38 %

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