› 6y60

X-ray diffraction
1.8Å resolution

Structure of Human Polyomavirus 12 VP1 in complex with 3'-Sialyllactosamine

Released:
DOI: 10.2210/pdb6y60/pdb
PDB entry 6y60 coloured by chain, front view.
PDB entry 6y60 coloured by chain, side view.
PDB entry 6y60 coloured by chain, top view.
Source organism: Human polyomavirus 12
Primary publication:
Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.
Ströh LJ, Rustmeier NH, Blaum BS, Botsch J, Rößler P, Wedekink F, Lipkin WI, Mishra N, Stehle T
OpenAccess logo mBio 11 (2020)
PMID: 32723915

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126031 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Capsid protein VP1 Chains: AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ
Molecule details ›
Chains: AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ
Length: 277 amino acids
Theoretical weight: 30.71 KDa
Source organism: Human polyomavirus 12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: M4T5D3 (Residues: 28-300; Coverage: 75%)
Gene name: VP1
Sequence domains: Polyomavirus coat protein

Ligands and Environments

Carbohydrate polymer : NEW Components: SIA, GAL
Carbohydrate polymer
2 bound ligands:
Ligand PO4 5 x PO4
Ligand SIA 3 x SIA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 83.322Å b: 141.724Å c: 251.302Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.204 0.243
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Structural Insight into Non-Enveloped Virus Binding to Glycosaminoglycan Receptors: A Review.
Sorin et al. (2021)
3 more

2 mentions without citation

Molecular Recognition Insights of Sialic Acid Glycans by Distinct Receptors Unveiled by NMR and Molecular Modeling.
Soares et al. (2021)
1 more