+Open data
-Basic information
Entry | Database: PDB / ID: 1rpu | ||||||
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Title | Crystal Structure of CIRV p19 bound to siRNA | ||||||
Components |
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Keywords | RNA Binding Protein/RNA / RNAi / PROTEIN-RNA COMPLEX / RNA DOUBLE HELIX / RNA LENGTH RECOGNITION / 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 | ||||||
Biological species | Carnation Italian ringspot virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Vargason, J.M. / Szittya, G. / Burgyan, J. / Hall, T.M.T. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Size selective recognition of siRNA by an RNA silencing suppressor Authors: Vargason, J.M. / Szittya, G. / Burgyan, J. / Hall, T.M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rpu.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rpu.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/1rpu ftp://data.pdbj.org/pub/pdb/validation_reports/rp/1rpu | 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: 6680.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by Dharmacon #2: Protein | Mass: 19358.373 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carnation Italian ringspot virus / Genus: Tombusvirus / Gene: p19 / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q66104 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG MME 2000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 1, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 17767 / Num. obs: 17767 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.087 |
Reflection shell | Resolution: 2.5→2.59 Å / Rsym value: 0.381 / % possible all: 95.4 |
Reflection | *PLUS % possible obs: 98.8 % / Redundancy: 18.9 % / Num. measured all: 318939 / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS % possible obs: 95.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |