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Yorodumi- PDB-5zho: Human group C rotavirus VP8*s recognize type A histo-blood group ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zho | |||||||||||||||||||||||||||||||
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Title | Human group C rotavirus VP8*s recognize type A histo-blood group antigens as ligands | |||||||||||||||||||||||||||||||
Components | Outer capsid protein VP8*Keywords | VIRAL PROTEIN / group C rotavirus / VP8* / galactin-like / histo-blood group antigen | Function / homology | Function and homology information host cell rough endoplasmic reticulum / 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 C | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å | Authors | Sun, X. / Duan, Z. / Qi, J. | Funding support | China, 1items |
Citation | Journal: J. Virol. / Year: 2018 | Title: Human Group C Rotavirus VP8*s Recognize Type A Histo-Blood Group Antigens as Ligands. Authors: Sun, X. / Wang, L. / Qi, J. / Li, D. / Wang, M. / Cong, X. / Peng, R. / Chai, W. / Zhang, Q. / Wang, H. / Wen, H. / Gao, G.F. / Tan, M. / Duan, Z. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zho.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zho.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/5zho ftp://data.pdbj.org/pub/pdb/validation_reports/zh/5zho | HTTPS FTP |
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-Related structure data
Related structure data | 5zhgSC 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: 18738.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rotavirus C / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q82040 |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: 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: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6.5 Details: 0.1 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 1.5 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 36324 / % possible obs: 99 % / Redundancy: 12.8 % / Biso Wilson estimate: 14.19 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 28.586 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.565 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZHG Resolution: 1.401→37.789 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.47 Å2 / Biso mean: 20.1766 Å2 / Biso min: 7.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.401→37.789 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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