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Yorodumi- PDB-4yg0: Structural basis of glycan recognition in neonate-specific rotaviruses -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yg0 | |||||||||
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Title | Structural basis of glycan recognition in neonate-specific rotaviruses | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | VIRAL PROTEIN / rotavirus / structural biology / glycan | |||||||||
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 | Human rotavirus A | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.285 Å | |||||||||
Authors | Hu, L. / Prasad, B.V.V. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2015 Title: Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus. Authors: Hu, L. / Ramani, S. / Czako, R. / Sankaran, B. / Yu, Y. / Smith, D.F. / Cummings, R.D. / Estes, M.K. / Venkataram Prasad, B.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yg0.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yg0.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 4yg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/4yg0 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/4yg0 | HTTPS FTP |
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-Related structure data
Related structure data | 4yfwSC 4yfzC 4yg3C 4yg6C C: citing same article (ref.) S: Starting model for refinement |
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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: 18683.471 Da / Num. of mol.: 1 / Fragment: UNP residues 64-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rotavirus A / Strain: N155 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6RGK2 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#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: 1.96 Å3/Da / Density % sol: 37.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M NaCl, 0.1M Imidazole, 1.0M Potasium/Sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014 |
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→31.02 Å / Num. obs: 35249 / % possible obs: 92.2 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.28→1.35 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 6.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YFW Resolution: 1.285→31.02 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.91 / Phase error: 18.5 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.285→31.02 Å
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Refine LS restraints |
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LS refinement shell |
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