[English] 日本語
Yorodumi- PDB-6k2o: Structural basis of glycan recognition in globally predominant hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k2o | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structural basis of glycan recognition in globally predominant human P[8] rotavirus | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | VIRAL PROTEIN / glycan binding specificity / VP8* structure / mucin core 2 / lacto-N-fucopentaose 1 (LNFP1) | |||||||||
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: 2.296 Å | |||||||||
Authors | Duan, Z. / Sun, X. | |||||||||
Funding support | China, 1items
| |||||||||
Citation | Journal: Virol Sin / Year: 2020 Title: Structural Basis of Glycan Recognition in Globally Predominant Human P[8] Rotavirus. Authors: Sun, X. / Dang, L. / Li, D. / Qi, J. / Wang, M. / Chai, W. / Zhang, Q. / Wang, H. / Bai, R. / Tan, M. / Duan, Z. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6k2o.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6k2o.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 6k2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k2o_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6k2o_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6k2o_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 6k2o_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/6k2o ftp://data.pdbj.org/pub/pdb/validation_reports/k2/6k2o | HTTPS FTP |
-Related structure data
Related structure data | 6k2nC 5jdbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18892.783 Da / Num. of mol.: 1 / Fragment: UNP residues 65-223 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus A Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: E2EA82 |
---|---|
#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 Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.33 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Sodium acetate trihydrate pH 4.5, 2.0M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 113 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.296→50 Å / Num. obs: 10510 / % possible obs: 100 % / Redundancy: 25.8 % / Biso Wilson estimate: 29.25 Å2 / Rmerge(I) obs: 0.159 / Rsym value: 0.159 / Net I/σ(I): 22.524 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 4.889 / Num. unique obs: 10510 / Rsym value: 0.86 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JDB Resolution: 2.296→44.711 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.296→44.711 Å
| ||||||||||||||||||
LS refinement shell | Resolution: 2.296→2.5 Å
|