› 3nxd

X-ray diffraction
2Å resolution

JC polyomavirus VP1 in complex with LSTc

Released:
DOI: 10.2210/pdb3nxd/pdb
PDB entry 3nxd coloured by chain, front view.
PDB entry 3nxd coloured by chain, side view.
PDB entry 3nxd coloured by chain, top view.
Source organism: JC polyomavirus
Primary publication:
Structure-function analysis of the human JC polyomavirus establishes the LSTc pentasaccharide as a functional receptor motif.
Neu U, Maginnis MS, Palma AS, Ströh LJ, Nelson CD, Feizi T, Atwood WJ, Stehle T
Cell Host Microbe 8 309-19 (2010)
PMID: 20951965

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo pentamer (preferred)
homo decamer
Assembly name:
PDBe Complex ID:
PDB-CPX-136562 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Major capsid protein VP1 Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 272 amino acids
Theoretical weight: 30.08 KDa
Source organism: JC polyomavirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P03089 (Residues: 23-290; Coverage: 76%)
Sequence domains: Polyomavirus coat protein
Structure domains: Capsid protein VP1,Polyomavirus

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, GAL, NAG, SIA
Carbohydrate polymer
2 bound ligands:
Ligand GOL 5 x GOL
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 149.67Å b: 96.34Å c: 128.22Å
α: 90° β: 110.28° γ: 90°
R-values:
R R work R free
0.18 0.178 0.206
Expression system: Escherichia coli

Quick links

Citations

49 review citations

Molecular biology, epidemiology, and pathogenesis of progressive multifocal leukoencephalopathy, the JC virus-induced demyelinating disease of the human brain.
Ferenczy et al. (2012)
48 more

9 mentions without citation

Viruses and sialic acids: rules of engagement.
Neu et al. (2011)
8 more