+Open data
-Basic information
Entry | Database: PDB / ID: 5vx9 | |||||||||
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Title | VP8* of P[6] Human Rotavirus RV3 in complex with LNFP1 | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | VIRAL PROTEIN / Glycan / HBGA / rotavirus | |||||||||
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: 1.822 Å | |||||||||
Authors | Hu, L. / Venkataram Prasad, B.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Glycan recognition in globally dominant human rotaviruses. Authors: Hu, L. / Sankaran, B. / Laucirica, D.R. / Patil, K. / Salmen, W. / Ferreon, A.C.M. / Tsoi, P.S. / Lasanajak, Y. / Smith, D.F. / Ramani, S. / Atmar, R.L. / Estes, M.K. / Ferreon, J.C. / Prasad, B.V.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vx9.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vx9.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 5vx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/5vx9 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/5vx9 | HTTPS FTP |
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-Related structure data
Related structure data | 5vx4C 5vx5C 5vx8C 2aenS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18483.477 Da / Num. of mol.: 1 / Fragment: UNP residues 65-223 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rotavirus A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D7F7M7 | ||
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-L-fucopyranose-(1-2)-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: Chemical | #4: 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: 2 Å3/Da / Density % sol: 38.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.0 M ammonium sulfate, 0.1 M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: Dec 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.822→31.74 Å / Num. obs: 13693 / % possible obs: 98.8 % / Redundancy: 1.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.046 / Net I/σ(I): 11.62 |
Reflection shell | Highest resolution: 1.822 Å / Rmerge(I) obs: 0.183 / CC1/2: 0.962 / Rpim(I) all: 0.091 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2AEN Resolution: 1.822→31.74 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 16.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.822→31.74 Å
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Refine LS restraints |
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LS refinement shell |
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