› 6c6q

X-ray diffraction
2Å resolution

Crystal Structure of the Murine Norovirus VP1 P Domain in complex with the CD300lf Receptor

Released:
DOI: 10.2210/pdb6c6q/pdb
Model geometry
Fit model/data
PDB entry 6c6q coloured by chain, front view.
PDB entry 6c6q coloured by chain, side view.
PDB entry 6c6q coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor.
Nelson CA, Wilen CB, Dai YN, Orchard RC, Kim AS, Stegeman RA, Hsieh LL, Smith TJ, Virgin HW, Fremont DH
OpenAccess logo Proc Natl Acad Sci U S A 115 E9201-E9210 (2018)
PMID: 30194229

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180326 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Capsid protein VP1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 303 amino acids
Theoretical weight: 32.96 KDa
Source organism: Murine norovirus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q80J94 (Residues: 229-531; Coverage: 56%)
Gene name: ORF2
Sequence domains: Calicivirus coat protein C-terminal
Structure domains:
CMRF35-like molecule 1 Chains: D, F
Molecule details ›
Chains: D, F
Length: 113 amino acids
Theoretical weight: 12.79 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6SJQ7 (Residues: 20-128; Coverage: 34%)
  • Best match: Q6SJQ7-2 (Residues: 20-131)
Gene names: Cd300lf, Clm1, Lmir3
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand EDO 22 x EDO
Ligand CL 2 x CL
Ligand MG 6 x MG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 48.712Å b: 135.245Å c: 139.516Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.182 0.222
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

20 review citations

Norovirus Attachment and Entry.
Graziano et al. (2019)
19 more

7 mentions without citation

The Antigenic Topology of Norovirus as Defined by B and T Cell Epitope Mapping: Implications for Universal Vaccines and Therapeutics.
van Loben Sels et al. (2019)
6 more