+Open data
-Basic information
Entry | Database: PDB / ID: 4li4 | ||||||
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Title | Crystal structure of HCoV-OC43 N-NTD complexed with AMP | ||||||
Components | Nucleoprotein | ||||||
Keywords | RNA BINDING PROTEIN / RNA-binding / AMP / Coronavirus / Nucleocapsid protein / N-terminal domain | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Human coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Lin, S.Y. / Liu, C.L. / Hou, M.H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target Authors: Lin, S.Y. / Liu, C.L. / Chang, Y.M. / Zhao, J. / Perlman, S. / Hou, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4li4.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4li4.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 4li4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/4li4 ftp://data.pdbj.org/pub/pdb/validation_reports/li/4li4 | HTTPS FTP |
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-Related structure data
Related structure data | 4kxjC 4lm7C 4lm9C 4lmcC 4j3kS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15437.901 Da / Num. of mol.: 1 / Fragment: UNP residues 55-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus / Strain: OC43Human coronavirus OC43 / Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SA23, UniProt: P33469*PLUS |
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#2: Chemical | ChemComp-AMP / |
#3: 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: 2.69 Å3/Da / Density % sol: 54.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2M SPG, 25% PEG1500, 5mM AMP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2011 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→30 Å / Num. obs: 17535 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.46 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.03 |
Reflection shell | Highest resolution: 1.71 Å / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J3K Resolution: 1.71→26.814 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7822 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 28.5 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.63 Å2 / Biso mean: 30.6922 Å2 / Biso min: 11.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→26.814 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: 10
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