+Open data
-Basic information
Entry | Database: PDB / ID: 4k7e | ||||||
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Title | Crystal structure of Junin virus nucleoprotein | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / alpha/beta/alpha sandwich / nucleoprotein | ||||||
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 / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Junin virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zhang, Y.J. / Li, L. / Liu, X. / Dong, S.S. / Wang, W.M. / Huo, T. / Rao, Z.H. / Yang, C. | ||||||
Citation | Journal: J.Gen.Virol. / Year: 2013 Title: Crystal structure of Junin virus nucleoprotein Authors: Zhang, Y.J. / Li, L. / Liu, X. / Dong, S.S. / Wang, W.M. / Huo, T. / Guo, Y. / Rao, Z.H. / Yang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k7e.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k7e.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/4k7e ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k7e | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26667.738 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, residues 341-564 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Junin virus / Gene: N / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6IVU2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.16 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris, 2.2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.26 Å / Num. all: 11382 / Num. obs: 11370 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 32.11 Å2 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 53.5 / Num. unique all: 11382 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.256 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8133 / SU ML: 0.23 / σ(F): 0 / Phase error: 24.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.851 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.72 Å2 / Biso mean: 41.8034 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→39.256 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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