› 3vyk

X-ray diffraction
1.5Å resolution

Crystal structure of C-type lectin domain of murine dendritic cell inhibitory receptor 2 in complex with N-glycan

Released:
DOI: 10.2210/pdb3vyk/pdb
PDB entry 3vyk coloured by chain, front view.
PDB entry 3vyk coloured by chain, side view.
PDB entry 3vyk coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Recognition of bisecting N-acetylglucosamine: structural basis for asymmetric interaction with the mouse lectin dendritic cell inhibitory receptor 2.
Nagae M, Yamanaka K, Hanashima S, Ikeda A, Morita-Matsumoto K, Satoh T, Matsumoto N, Yamamoto K, Yamaguchi Y
J Biol Chem 288 33598-33610 (2013)
PMID: 24108122

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178535 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
C-type lectin domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 129 amino acids
Theoretical weight: 14.96 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5YIR8 (Residues: 107-233; Coverage: 54%)
Gene names: Clec4a4, Dcir2
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A

Ligands and Environments

Carbohydrate polymer : NEW Components: MMA, MAN, NAG
Carbohydrate polymer
3 bound ligands:
Ligand CA 1 x CA
Ligand SO4 2 x SO4
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P3221
Unit cell:
a: 76.341Å b: 76.341Å c: 50.556Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.21 0.224
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Sugar recognition and protein-protein interaction of mammalian lectins conferring diverse functions.
Nagae et al. (2015)
4 more

6 mentions without citation

Recent insights into structures and functions of C-type lectins in the immune system.
Drickamer et al. (2015)
5 more