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PDBsum entry 5b1x
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Carbohydrate binding protein
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PDB id
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5b1x
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PDB id:
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| Name: |
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Carbohydrate binding protein
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Title:
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Crystal structure of human dendritic cell inhibitory receptor (dcir) c-type lectin domain in complex with biantennary glycan
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Structure:
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C-type lectin domain family 4 member a. Chain: a, b, c, d. Fragment: unp residues 106-237. Synonym: c-type lectin ddb27,c-type lectin superfamily member 6, dendritic cell immunoreceptor,lectin-like immunoreceptor. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: clec4a, clecsf6, dcir, llir, hdcgc13p. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.90Å
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R-factor:
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0.262
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R-free:
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0.290
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Authors:
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M.Nagae,Y.Yamaguchi
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Key ref:
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M.Nagae
et al.
(2016).
Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan.
Febs Lett,
590,
1280-1288.
PubMed id:
DOI:
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Date:
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21-Dec-15
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Release date:
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11-May-16
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PROCHECK
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Headers
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References
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Q9UMR7
(CLC4A_HUMAN) -
C-type lectin domain family 4 member A from Homo sapiens
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Seq:
Struc:
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237 a.a.
130 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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DOI no:
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Febs Lett
590:1280-1288
(2016)
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PubMed id:
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Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan.
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M.Nagae,
A.Ikeda,
S.Hanashima,
T.Kojima,
N.Matsumoto,
K.Yamamoto,
Y.Yamaguchi.
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ABSTRACT
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Human dendritic cell inhibitory receptor (DCIR) is a C-type lectin receptor
expressed in classical dendritic cells and accepts several oligosaccharide
ligands including N-glycans. Here, we report the crystal structures of human
DCIR C-type lectin domains in the absence and presence of a branched N-glycan
unit. The domain has a typical C-type lectin fold and two bound calcium ions. In
the ligand-bound form, the disaccharide unit (GlcNAcβ1-2Man) acceptably fits
the electron density map, indicating that it forms the main epitope. The
recognition of the nonterminal N-glycan unit explains the relatively broad
specificity of this lectin.
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