› 5b1x

X-ray diffraction
2.9Å resolution

Crystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in complex with biantennary glycan

Released:
DOI: 10.2210/pdb5b1x/pdb
PDB entry 5b1x coloured by chain, front view.
PDB entry 5b1x coloured by chain, side view.
PDB entry 5b1x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan.
Nagae M, Ikeda A, Hanashima S, Kojima T, Matsumoto N, Yamamoto K, Yamaguchi Y
FEBS Lett 590 1280-8 (2016)
PMID: 27015765

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-193970 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
C-type lectin domain family 4 member A Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 134 amino acids
Theoretical weight: 15.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UMR7 (Residues: 106-237; Coverage: 56%)
Gene names: CLEC4A, CLECSF6, DCIR, HDCGC13P, LLIR
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN, NAG
Carbohydrate polymer
1 bound ligand:
Ligand CA 8 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21212
Unit cell:
a: 102.669Å b: 104.845Å c: 65.354Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.262 0.26 0.29
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Human Dendritic Cells: Ontogeny and Their Subsets in Health and Disease.
Solano-Gálvez et al. (2018)
4 more

2 mentions without citation

New targets for HIV drug discovery.
Puhl et al. (2019)
1 more