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- PDB-4yfz: Structural basis of glycan recognition in neonate-specific rotaviruses -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yfz | |||||||||
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Title | Structural basis of glycan recognition in neonate-specific rotaviruses | |||||||||
![]() | Outer capsid protein VP4 | |||||||||
![]() | VIRAL PROTEIN / rotavirus / structural biology / glycan | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hu, L. / Prasad, B.V.V. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.8 KB | Display | ![]() |
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PDB format | ![]() | 39.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 727.4 KB | Display | ![]() |
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Full document | ![]() | 727.4 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yfwSC ![]() 4yg0C ![]() 4yg3C ![]() 4yg6C 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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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.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-3)-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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.94 M Sodium citrate 0.1 M Imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2013 |
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: 1.5→32.1 Å / Num. obs: 28272 / % possible obs: 99.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 6.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YFW Resolution: 1.5→32.095 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 19.87 / 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: 1.5→32.095 Å
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Refine LS restraints |
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LS refinement shell |
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