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Yorodumi- PDB-3cz3: Crystal structure of Tomato Aspermy Virus 2b in complex with siRNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cz3 | ||||||
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Title | Crystal structure of Tomato Aspermy Virus 2b in complex with siRNA | ||||||
Components |
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Keywords | VIRAL PROTEIN/RNA / protein-dsRNA complex / Coiled coil / Nucleus / Suppressor of RNA silencing / VIRAL PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information virus-mediated perturbation of host defense response / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Tomato aspermy virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.23 Å | ||||||
Authors | Ma, J.B. / Li, F. / Ding, S.W. / Patel, D.J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cz3.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cz3.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/3cz3 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3cz3 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 6077.673 Da / Num. of mol.: 2 / Fragment: ppi-1 / Source method: obtained synthetically #2: RNA chain | Mass: 6054.633 Da / Num. of mol.: 2 / Fragment: ppi-2 / Source method: obtained synthetically #3: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.2 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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 |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Redundancy: 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 |
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Reflection | Resolution: 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 shell | Resolution: 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 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.986 Å2
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Refinement step | Cycle: LAST / Resolution: 3.23→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.23→3.315 Å / Total num. of bins used: 20
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