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Yorodumi- PDB-5ymu: Functional and structural characterization of P[19] rotavirus VP8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ymu | ||||||
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Title | Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens | ||||||
Components | Outer capsid protein VP4 | ||||||
Keywords | VIRAL PROTEIN / Rotavirus / P[19] VP8* | ||||||
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 | Porcine rotavirus A | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sun, X. / Duan, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: J. Virol. / Year: 2018 Title: Glycan Binding Specificity and Mechanism of Human and Porcine P[6]/P[19] Rotavirus VP8*s. Authors: Sun, X. / Li, D. / Qi, J. / Chai, W. / Wang, L. / Wang, L. / Peng, R. / Wang, H. / Zhang, Q. / Pang, L. / Kong, X. / Wang, H. / Jin, M. / Gao, G.F. / Duan, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ymu.cif.gz | 292.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ymu.ent.gz | 239.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ymu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ymu_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 5ymu_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 5ymu_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 5ymu_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/5ymu ftp://data.pdbj.org/pub/pdb/validation_reports/ym/5ymu | HTTPS FTP |
-Related structure data
Related structure data | 5ymsC 5ymtC 5gj6S 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18513.578 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine rotavirus A Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: A0A2U8JDD5*PLUS #2: Chemical | #3: 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: 2.77 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES monohydrate pH 6.0, 25% w/v polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97775 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97775 Å / Relative weight: 1 |
Reflection | Resolution: 1.796→50 Å / Num. obs: 74097 / % possible obs: 100 % / Redundancy: 10.5 % / Net I/σ(I): 21.895 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GJ6 Resolution: 1.8→41.86 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.06 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.86 Å
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Refinement TLS params. | Method: refined / Origin x: 36.3251 Å / Origin y: -37.9375 Å / Origin z: 25.8261 Å
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Refinement TLS group | Selection details: ALL |