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Yorodumi- PDB-5yms: Structural basis of glycan specificity and identification of a no... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yms | |||||||||
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Title | Structural basis of glycan specificity and identification of a novel glycan binding cavity in human P[19] rotavirus | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | VIRAL PROTEIN / P[19] rotavirus / P[6] rotavirus / VP8* / Mucin core2core 2 / Lacto-N-tetrarosetetraose (LNT) | |||||||||
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: 2.1 Å | |||||||||
Authors | Sun, X. / Dandi, L. / 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 | 5yms.cif.gz | 538.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yms.ent.gz | 444.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yms_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 5yms_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 5yms_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 5yms_validation.cif.gz | 81.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/5yms ftp://data.pdbj.org/pub/pdb/validation_reports/ym/5yms | HTTPS FTP |
-Related structure data
Related structure data | 5ymtC 5ymuC 5gj6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 18253.311 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: P[19] VP8* and LNT / Source: (gene. exp.) Human rotavirus A Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: Q9Q2P6 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: 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: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% w/v polyethylene glycol MME 5000 |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 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: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 104019 / % possible obs: 99.9 % / Redundancy: 6.3 % / Net I/σ(I): 10.575 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GJ6 Resolution: 2.1→49.675 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 21.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.41 Å2 / Biso mean: 31.9 Å2 / Biso min: 11.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→49.675 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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