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Yorodumi- PDB-4o6h: 2.8A crystal structure of Lymphocytic Choriomeningitis Virus Nucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o6h | ||||||
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Title | 2.8A crystal structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-terminal Domain | ||||||
Components | Nucleoprotein | ||||||
Keywords | HYDROLASE / Exoribonuclease | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Lymphocytic choriomeningitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | West, B.R. / Hastie, K.M. / Saphire, E.O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of the LCMV nucleoprotein provides a template for understanding arenavirus replication and immunosuppression. Authors: West, B.R. / Hastie, K.M. / Saphire, E.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o6h.cif.gz | 577.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o6h.ent.gz | 481.9 KB | Display | PDB format |
PDBx/mmJSON format | 4o6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o6h_validation.pdf.gz | 514.7 KB | Display | wwPDB validaton report |
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Full document | 4o6h_full_validation.pdf.gz | 521.8 KB | Display | |
Data in XML | 4o6h_validation.xml.gz | 53.3 KB | Display | |
Data in CIF | 4o6h_validation.cif.gz | 70 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/4o6h ftp://data.pdbj.org/pub/pdb/validation_reports/o6/4o6h | HTTPS FTP |
-Related structure data
Related structure data | 4o6iC 3q7cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26400.145 Da / Num. of mol.: 8 / Fragment: C-Terminal Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymphocytic choriomeningitis virus / Strain: Armstrong / Gene: N / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / References: UniProt: P09992 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-IMD / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-K / |
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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: 2.94 Å3/Da / Density % sol: 58.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.35M potassium phosphate, 20% PEG 3350, cryoprotected with 20% glycerol, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.264 Å / Num. all: 60576 / Num. obs: 58941 / % possible obs: 97.3 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3Q7C Resolution: 2.8→47.264 Å / SU ML: 0.46 / σ(F): 1.36 / Phase error: 35.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→47.264 Å
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Refine LS restraints |
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LS refinement shell |
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