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- PDB-4jnx: Crystal structure of RNA silencing suppressor p19 complexed with ... -

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Basic information

Entry
Database: PDB / ID: 4jnx
TitleCrystal structure of RNA silencing suppressor p19 complexed with double-helical RNA 20mer pG(CUG)6C
Components
  • 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
  • RNA silencing suppressor p19
KeywordsRNA BINDING PROTEIN/RNA / RNA silencing suppression / trinucleotide repeats / protein-RNA complex / dimer / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


virion component / 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: 1.95 Å
AuthorsKatorcha, E. / 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
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 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 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
D: RNA silencing suppressor p19
B: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
G: 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,14910
Polymers41,7164
Non-polymers4336
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-123 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.917, 89.917, 148.353
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-420-

HOH

21A-429-

HOH

31A-437-

HOH

41D-425-

HOH

51D-462-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22G

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label alt-ID
11SERSERPROPRO1AA2 - 1272 - 127
21SERSERPROPRO1DB2 - 1272 - 127
12GGCC4BC401 - 4201 - 20B
22GGCC4GD401 - 4201 - 20B

NCS ensembles :
ID
1
2
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.: 2 / 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
#2: RNA chain 5'-R(P*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*CP*UP*GP*C)-3'


Mass: 6344.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: siRNA pG(CUG)6C
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 291 K / pH: 6
Details: 1.6 M ammonium sulfate, pH 8, potassium chloride, MES/NaOH, trace magnesium, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98035 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98035 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11K, H, -L20.5
ReflectionResolution: 1.95→20 Å / Num. all: 32588 / Num. obs: 32285 / % possible obs: 98.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.072 / Χ2: 1.051 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.022.90.72616281.121198.2
2.02-2.12.90.5616541.238197.9
2.1-2.22.90.38716731.02198.6
2.2-2.312.90.28116741.258198.6
2.31-2.462.90.216601.04199.1
2.46-2.652.90.14917081.048199.4
2.65-2.912.90.09416851.01199.6
2.91-3.332.90.05317090.96199.7
3.33-4.192.80.04317191.053199.4
4.19-202.70.03517780.762198.8

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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
Starting model: PDB ENTRY 1R9F

1r9f


Resolution: 1.95→19.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2369 / WRfactor Rwork: 0.2006 / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.8381 / SU B: 6.67 / SU ML: 0.109 / SU R Cruickshank DPI: 0.0421 / SU Rfree: 0.0352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 1632 5.1 %RANDOM
Rwork0.1962 ---
obs0.1981 30613 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.1 Å2 / Biso mean: 36.6245 Å2 / Biso min: 21.36 Å2
Baniso -1Baniso -2Baniso -3
1-12.18 Å20 Å20 Å2
2--12.18 Å20 Å2
3----24.35 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 844 22 223 3093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0163914
X-RAY DIFFRACTIONr_bond_other_d0.0060.022636
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.6215678
X-RAY DIFFRACTIONr_angle_other_deg1.44536158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85322.157102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98715336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0291520
X-RAY DIFFRACTIONr_chiral_restr0.2090.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023224
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02934
X-RAY DIFFRACTIONr_mcbond_it2.1983.009988
X-RAY DIFFRACTIONr_mcbond_other2.1993.005987
X-RAY DIFFRACTIONr_mcangle_it3.0064.4781228
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1941TIGHT THERMAL1.140.5
21B586MEDIUM POSITIONAL0.030.5
21B586MEDIUM THERMAL0.462
22B616MEDIUM POSITIONAL0.030.5
22B616MEDIUM THERMAL0.572
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 96 -
Rwork0.284 2242 -
all-2338 -
obs--98.4 %
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)
10.1515-0.0196-0.14760.12570.08870.5274-0.0057-0.004-0.0097-0.0024-0.00780.0094-0.02230.0220.01350.0046-0.00290.00320.0032-0.00230.00518.516832.0596-0.0002
20.2797-0.09710.40390.1218-0.2510.809-0.015-0.01280.0582-0.0083-0.0129-0.0309-0.05620.0330.02790.0624-0.00520.01290.0515-0.00890.107326.751546.3161-0.0056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 127
2X-RAY DIFFRACTION1D2 - 127
3X-RAY DIFFRACTION2B401 - 420
4X-RAY DIFFRACTION2G401 - 420

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