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- PDB-4yfw: 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: 4yfw | ||||||
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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 | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 66 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.1 KB | Display | ![]() |
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Full document | ![]() | 411.8 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yfzC ![]() 4yg0C ![]() 4yg3C ![]() 4yg6C ![]() 4drvS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18683.471 Da / Num. of mol.: 2 / Fragment: UNP residues 64-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% PEG 8000 0.1 M CHES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2012 |
Radiation | Monochromator: Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→36.53 Å / Num. obs: 34723 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.3 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DRV Resolution: 1.66→36.53 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.59 / Phase error: 25.06 / 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: 1.66→36.53 Å
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Refine LS restraints |
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LS refinement shell |
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