› 4fmj

X-ray diffraction
2.4Å resolution

Merkel cell polyomavirus VP1 in complex with GD1a oligosaccharide

Released:
DOI: 10.2210/pdb4fmj/pdb
PDB entry 4fmj coloured by chain, front view.
PDB entry 4fmj coloured by chain, side view.
PDB entry 4fmj coloured by chain, top view.
Source organism: Merkel cell polyomavirus
Primary publication:
Structures of Merkel cell polyomavirus VP1 complexes define a sialic acid binding site required for infection.
Neu U, Hengel H, Blaum BS, Schowalter RM, Macejak D, Gilbert M, Wakarchuk WW, Imamura A, Ando H, Kiso M, Arnberg N, Garcea RL, Peters T, Buck CB, Stehle T
PLoS Pathog 8 e1002738 (2012)
PMID: 22910713

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo pentamer
homo decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110986 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
VP1 Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Length: 289 amino acids
Theoretical weight: 31.93 KDa
Source organism: Merkel cell polyomavirus
Expression system: Escherichia coli
UniProt:
  • Canonical: C0JPK1 (Residues: 37-319; Coverage: 67%)
Gene name: VP1
Sequence domains: Polyomavirus coat protein
Structure domains: Capsid protein VP1,Polyomavirus

Ligands and Environments

Carbohydrate polymer : NEW Components: SIA, GAL
Carbohydrate polymer
3 bound ligands:
Ligand GOL 8 x GOL
Ligand CL 20 x CL
Ligand SIA 1 x SIA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P1
Unit cell:
a: 84.66Å b: 130.15Å c: 165.53Å
α: 98.04° β: 101.02° γ: 105.81°
R-values:
R R work R free
0.193 0.192 0.246
Expression system: Escherichia coli

Quick links

Citations

21 review citations

The sweet spot: defining virus-sialic acid interactions.
Stencel-Baerenwald et al. (2014)
20 more

4 mentions without citation

Structures of Merkel cell polyomavirus VP1 complexes define a sialic acid binding site required for infection.
Neu et al. (2012)
3 more