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Yorodumi- PDB-2gib: Crystal structure of the SARS coronavirus nucleocapsid protein di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gib | ||||||
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Title | Crystal structure of the SARS coronavirus nucleocapsid protein dimerization domain | ||||||
Components | Nucleocapsid protein | ||||||
Keywords | VIRAL PROTEIN / SARS / nucleocapsid / dimer | ||||||
Function / homology | Function and homology information SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / viral capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / molecular adaptor activity / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / host cell nucleus / DNA binding / RNA binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Yu, I.M. / Oldham, M.L. / Zhang, J. / Chen, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Crystal structure of the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein dimerization domain reveals evolutionary linkage between corona- and arteriviridae. Authors: Yu, I.M. / Oldham, M.L. / Zhang, J. / Chen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gib.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gib.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/2gib ftp://data.pdbj.org/pub/pdb/validation_reports/gi/2gib | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biologic assembly is a dimer as found in the asymmetric unit |
-Components
#1: Protein | Mass: 11554.877 Da / Num. of mol.: 2 / Fragment: dimerization domain (residues 270-370) Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Gene: N / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P59595 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54.38 % |
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Crystal grow | Temperature: 277.5 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30-33% Pentaerythritol ethoxylate 15/4 EO/OH, 50 mM Ammonium sulfate, 50 mM Bis-Tris , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.5K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97940, 0.94285 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2005 | ||||||||||||
Radiation | Monochromator: Rosenbaum-Rock monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→30.93 Å / Num. all: 23293 / Num. obs: 23088 / % possible obs: 99.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||
Reflection shell | Resolution: 1.75→1.795 Å / % possible all: 96.12 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→30.93 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.535 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 17.965 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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