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- PDB-2ge8: Structure of the C-terminal dimerization domain of infectious bro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ge8 | ||||||
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Title | Structure of the C-terminal dimerization domain of infectious bronchitis virus nucleocapsid protein | ||||||
![]() | Nucleocapsid protein | ||||||
![]() | VIRUS/VIRAL PROTEIN/RNA BINDING PROTEIN / Nucleocapsid protein / N protein / Coronavirus / IBV N protein / Dimerization domain / VIRUS-VIRAL PROTEIN-RNA BINDING PROTEIN COMPLEX | ||||||
Function / homology | ![]() host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collisson, E.W. / Lescar, J. / Prasad, B.V. | ||||||
![]() | ![]() Title: X-ray structures of the N- and C-terminal domains of a coronavirus nucleocapsid protein: implications for nucleocapsid formation. Authors: Jayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collisson, E.W. / Lescar, J. / Prasad, B.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.5 KB | Display | ![]() |
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PDB format | ![]() | 141.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2c86C ![]() 2ca1C ![]() 2ge7SC ![]() 2gecC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | Dimer in solution and 4 dimers in assymetric unit. Hypothesized dimer-dimer interaction to form linaer arrays seen in assymetric unit with 8 molecules |
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Components
#1: Protein | Mass: 12849.602 Da / Num. of mol.: 8 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 30% PEG 4000, 100 mM Tris-HCl pH 8.6, 800 mM LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 178 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 19, 2003 Details: Bent conical Si-mirror (Rh coated). Bent Ge(111) monochromator |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→129.473 Å / Num. all: 69504 / Num. obs: 66258 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2→2.11 Å / % possible obs: 97.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 0.5 / Num. measured all: 35383 / Num. unique obs: 9713 / Rsym value: 0.01276 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2GE7 4 copies Resolution: 2.2→47.78 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.884 / SU B: 7.789 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.309 / ESU R Free: 0.247 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.178 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→47.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.199→2.256 Å / Total num. of bins used: 20
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