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- PDB-3cz3: Crystal structure of Tomato Aspermy Virus 2b in complex with siRNA -

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Basic information

Entry
Database: PDB / ID: 3cz3
TitleCrystal structure of Tomato Aspermy Virus 2b in complex with siRNA
Components
  • Protein 2b
  • RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*A)-3')
  • RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*G)-3')
KeywordsVIRAL PROTEIN/RNA / protein-dsRNA complex / Coiled coil / Nucleus / Suppressor of RNA silencing / VIRAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


host cell nucleus / RNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3800 / Cucumovirus protein 2B / Cucumovirus protein 2B / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Suppressor of silencing 2b
Similarity search - Component
Biological speciesTomato aspermy virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.23 Å
AuthorsMa, J.B. / Li, F. / Ding, S.W. / Patel, D.J.
CitationJournal: To be Published
Title: Structural Basis for siRNA Recognition by 2b, a Viral Suppressor of Non-Cell Autonomous RNA Silencing
Authors: Ma, J.B. / Li, F. / Ding, S.W. / Patel, D.J.
History
DepositionApr 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*A)-3')
F: RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*G)-3')
G: RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*A)-3')
H: RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*G)-3')
A: Protein 2b
B: Protein 2b
C: Protein 2b
D: Protein 2b


Theoretical massNumber of molelcules
Total (without water)57,4868
Polymers57,4868
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18170 Å2
ΔGint-108.8 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.900, 165.670, 35.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 6077.673 Da / Num. of mol.: 2 / Fragment: ppi-1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*G)-3')


Mass: 6054.633 Da / Num. of mol.: 2 / Fragment: ppi-2 / Source method: obtained synthetically
#3: Protein
Protein 2b


Mass: 8305.397 Da / Num. of mol.: 4 / Fragment: Tav2b N69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato aspermy virus / Gene: RNA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q8UYT3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 20% PEG 4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 5.0, VAPOR DIFFUSION, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ammonium sulfate11
3sodium acetate11
4PEG 400012
5ammonium sulfate12
6sodium acetate12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97907, 0.97927, 0.96411
SYNCHROTRONAPS 24-ID-C20.97918
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 19, 2006
ADSC QUANTUM 3152CCDOct 18, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.979271
30.964111
40.979181
ReflectionRedundancy: 6.1 % / Av σ(I) over netI: 14.7 / Number: 103017 / Rmerge(I) obs: 0.052 / Χ2: 1.03 / D res high: 3.3 Å / D res low: 30 Å / Num. obs: 16831 / % possible obs: 87.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.083098.110.0341.0277.4
5.637.0810010.0620.9887.6
4.925.6397.110.0561.0347
4.484.9286.110.0561.016.5
4.164.4883.110.0591.0696.3
3.914.1686.110.0781.0665.7
3.723.9191.110.0990.995.5
3.553.7284.610.1291.0425.1
3.423.5581.610.1621.0254.8
3.33.4268.210.171.0444.7
ReflectionResolution: 3.2→50 Å / Num. all: 12056 / Num. obs: 10597 / % possible obs: 87.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Χ2: 1.04 / Net I/σ(I): 10.7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.6 / Num. unique all: 803 / Rsym value: 0.574 / Χ2: 1.081 / % possible all: 69.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 3.23→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 40.541 / SU ML: 0.681 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.899 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 755 9.5 %RANDOM
Rwork0.226 ---
obs0.231 7907 65 %-
all-12056 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.986 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--0.65 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 3.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 3240 0 0 5166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215566
X-RAY DIFFRACTIONr_angle_refined_deg1.4672.6688205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7585218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46721.786112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.8815449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5061536
X-RAY DIFFRACTIONr_chiral_restr0.120.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023004
X-RAY DIFFRACTIONr_nbd_refined0.220.21403
X-RAY DIFFRACTIONr_nbtor_refined0.290.23001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.21
X-RAY DIFFRACTIONr_mcbond_it0.491.51158
X-RAY DIFFRACTIONr_mcangle_it0.90721787
X-RAY DIFFRACTIONr_scbond_it0.54635946
X-RAY DIFFRACTIONr_scangle_it1.0514.56418
LS refinement shellResolution: 3.23→3.315 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.924 13 -
Rwork0.498 124 -
all-137 -
obs--16.02 %

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