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Yorodumi- PDB-4yg6: Structural basis of glycan recognition in neonate-specific rotaviruses -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yg6 | |||||||||||||||||||||||||||||||
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Title | Structural basis of glycan recognition in neonate-specific rotaviruses | |||||||||||||||||||||||||||||||
Components | Outer capsid protein VP8*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 | Rotavirus A | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | Authors | Hu, L. / Prasad, B.V.V. | Funding support | United States, 1items |
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 | 4yg6.cif.gz | 178.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yg6.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 4yg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yg6_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4yg6_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4yg6_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 4yg6_validation.cif.gz | 68.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/4yg6 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/4yg6 | HTTPS FTP |
-Related structure data
Related structure data | 4yfwC 4yfzC 4yg0C 4yg3SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18063.570 Da / Num. of mol.: 4 / Fragment: UNP residues 65-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus A Strain: isolate Cow/United States/B223/1983 G10-P8[11]-I2-Rx-Cx-Mx-A13-Nx-Tx-E2-Hx Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35746, UniProt: A2T3T2*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-PO4 / #5: 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: 1.92 Å3/Da / Density % sol: 35.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.1 M Phosphate citrate, 1.6 M Sodium dihydrogen phosphate, 0.4 M di-Potassium hydrogen phosphate. |
-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: Jan 24, 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: 1.46→36.2 Å / Num. obs: 93062 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 4.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YG3 Resolution: 1.46→36.2 Å / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 21.97 / Stereochemistry target values: TWIN_LSQ_F
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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: 1.46→36.2 Å
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Refine LS restraints |
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LS refinement shell |
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