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Open data
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Basic information
Entry | Database: PDB / ID: 4lmc | ||||||
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Title | Crystal structure of HCoV-OC43 N-NTD complexed with CMP | ||||||
![]() | Nucleoprotein | ||||||
![]() | RNA BINDING PROTEIN / HCoV-OC43 / Nucleocapsid protein / N-terminal domain / RNA binding | ||||||
Function / homology | ![]() host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, S.Y. / Liu, C.L. / Hou, M.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.8 KB | Display | ![]() |
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PDB format | ![]() | 48.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 753.6 KB | Display | ![]() |
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Full document | ![]() | 759 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kxjC ![]() 4li4C ![]() 4lm7C ![]() 4lm9C ![]() 4j3kS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15350.822 Da / Num. of mol.: 1 / Fragment: UNP residues 55-187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-C5P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG1500, 0.25M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.74→30 Å / Num. all: 16152 / Num. obs: 16152 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.72 Å2 |
Reflection shell | Resolution: 1.74→1.8 Å / % possible all: 94.8 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4J3K Resolution: 1.742→26.807 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8157 / SU ML: 0.21 / σ(F): 1.37 / Phase error: 25.42 / Stereochemistry target values: Engh & Huber
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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: 85.81 Å2 / Biso mean: 33.1738 Å2 / Biso min: 11.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.742→26.807 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: 12
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