› 5yms

X-ray diffraction
2.1Å resolution

Structural basis of glycan specificity and identification of a novel glycan binding cavity in human P[19] rotavirus

Released:
DOI: 10.2210/pdb5yms/pdb
PDB entry 5yms coloured by chain, front view.
PDB entry 5yms coloured by chain, side view.
PDB entry 5yms coloured by chain, top view.
Source organism: Human rotavirus A
Primary publication:
Glycan Binding Specificity and Mechanism of Human and Porcine P[6]/P[19] Rotavirus VP8*s.
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 GF, Duan Z
J Virol 92 (2018)
PMID: 29720519

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192970 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Outer capsid protein VP8* Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 161 amino acids
Theoretical weight: 18.25 KDa
Source organism: Human rotavirus A
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: Q9Q2P6 (Residues: 64-223; Coverage: 21%)
Sequence domains: Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain
Structure domains: Jelly Rolls

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, A2G, GAL
Carbohydrate polymer
1 bound ligand:
Ligand NAG 6 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2
Unit cell:
a: 179.776Å b: 129.346Å c: 86.365Å
α: 90° β: 116.07° γ: 90°
R-values:
R R work R free
0.183 0.181 0.213
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4

Quick links

Citations

4 review citations

Glycan Microarrays as Chemical Tools for Identifying Glycan Recognition by Immune Proteins.
Gao et al. (2019)
3 more

3 mentions without citation

Structural Basis of Glycan Recognition of Rotavirus.
Sun et al. (2021)
2 more