5VC1 image
Entry Detail
PDB ID:
5VC1
Keywords:
Title:
Crystal structure of L-selectin lectin/EGF domains
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2017-03-30
Release Date:
2017-06-14
Method Details:
Experimental Method:
Resolution:
1.94 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
I 2 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:L-selectin
Mutations:N22Q, N139Q
Chain IDs:A
Chain Length:157
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Reducing Macro- and Microheterogeneity of N-Glycans Enables the Crystal Structure of the Lectin and EGF-Like Domains of Human L-Selectin To Be Solved at 1.9 angstrom Resolution.
Chembiochem 18 1338 1345 (2017)
PMID: 28489325 DOI: 10.1002/cbic.201700220

Abstact

L-Selectin, a cell-adhesion receptor on the surface of most leukocytes, contains seven N-glycosylation sites. In order to obtain the crystal structure of human L-selectin, we expressed a shortened version of L-selectin comprising the C-type lectin and EGF-like domains (termed LE) and systematically analysed mutations of the three glycosylation sites (Asn22, Asn66 and Asn139) in order to reduce macroheterogeneity. After we further removed microheterogeneity, we obtained crystals that diffracted X-rays up to 1.9 Å from a variant (LE010) with exchanges N22Q and N139Q and one GlcNAc2 Man5 N-glycan chain attached to Asn66. Crystal-structure analysis showed that the terminal mannose of GlcNAc2 Man5 of one LE010 molecule was coordinated to Ca2+ in the binding site of a symmetry-related LE010. The orientation of the lectin and EGF-like domain was similar to the described "bent" conformation of E- and P-selectins. The Ca2+ -binding site reflects the binding mode seen in E- and P-selectin structures co-crystallised with ligands.

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