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Yorodumi- PDB-4g9z: Lassa nucleoprotein with dsRNA reveals novel mechanism for immune... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g9z | ||||||
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Title | Lassa nucleoprotein with dsRNA reveals novel mechanism for immune suppression | ||||||
Components |
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Keywords | VIRAL PROTEIN/RNA / Structural Genomics / Scottish Structural Proteomics Facility / SSPF / 3'-5'-ribonuclease / nuclease / VIRAL PROTEIN-RNA complex | ||||||
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 / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex ...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 / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Lassa virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å | ||||||
Authors | Jiang, X. / Huang, Q. / Wang, W. / Dong, H. / Ly, H. / Liang, Y. / Dong, C. / Scottish Structural Proteomics Facility (SSPF) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structures of Arenaviral Nucleoproteins with Triphosphate dsRNA Reveal a Unique Mechanism of Immune Suppression. Authors: Jiang, X. / Huang, Q. / Wang, W. / Dong, H. / Ly, H. / Liang, Y. / Dong, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g9z.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g9z.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 4g9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/4g9z ftp://data.pdbj.org/pub/pdb/validation_reports/g9/4g9z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 1215.794 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 1295.842 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 24013.627 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 364-569 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lassa virus / Strain: Josiah / Gene: N / Plasmid: pLou3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta cells / References: UniProt: P13699 |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 4.5 Details: 18% PEG MME 5000, 0.1M Na-citrate, pH4.5, 2.4% PEG MME350, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 196 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8726 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2011 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→39.22 Å / Num. obs: 15723 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 6.8 |
-Processing
Software |
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Refinement | Resolution: 2.03→54.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.983 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.387 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→54.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.083 Å / Total num. of bins used: 20
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