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Yorodumi- PDB-2i2s: Crystal Structure of the porcine CRW-8 rotavirus VP8* carbohydrat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i2s | ||||||
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Title | Crystal Structure of the porcine CRW-8 rotavirus VP8* carbohydrate-recognising domain | ||||||
Components | Outer capsid protein VP4 | ||||||
Keywords | VIRAL PROTEIN / beta-sandwich | ||||||
Function / homology | Function and homology information host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane Similarity search - Function | ||||||
Biological species | Porcine rotavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Blanchard, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Insight into Host Cell Carbohydrate-recognition by Human and Porcine Rotavirus from Crystal Structures of the Virion Spike Associated Carbohydrate-binding Domain (VP8*) Authors: Blanchard, H. / Yu, X. / Coulson, B.S. / von Itzstein, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8 Authors: Scott, S.A. / Holloway, G. / Coulson, B.S. / Szyczew, A.J. / Kiefel, M.J. / von Itzstein, M. / Blanchard, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i2s.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i2s.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 2i2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/2i2s ftp://data.pdbj.org/pub/pdb/validation_reports/i2/2i2s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological unit is a monomer of VP8* which forms part of the rotavirus spike protein (VP4). The spike protein is considered to be formed of a dimer (though some evidence suggests a trimer) of VP4. The crystallographic asymmetric unit contains two molecules of VP8*. |
-Components
-Protein / Sugars , 2 types, 5 molecules AB
#1: Protein | Mass: 18449.479 Da / Num. of mol.: 2 / Fragment: VP8* domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine rotavirus / Species: Rotavirus C / Strain: strain CRW-8 / Plasmid: pGex-VP8*(64-224) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 DE3 / References: UniProt: P11114, UniProt: P0C6Y8*PLUS #4: Sugar | |
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-Non-polymers , 5 types, 371 molecules
#2: Chemical | #3: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.59 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 70% MPD, 0.1M HEPES pH 7.5, methyl-alpha-D-N-acetylneuraminide , VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9794 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2004 / Details: mirrors |
Radiation | Monochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→55.9 Å / Num. obs: 17704 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model based on the structure of Rhesus rotavirus VP8* Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.307 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.243 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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