5VC1

Crystal structure of L-selectin lectin/EGF domains

Summary for 5VC1

• Entry DOI: 10.2210/pdb5vc1/pdb
• Descriptor: L-selectin, beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, TETRAETHYLENE GLYCOL, ... (7 entities in total)
• Functional Keywords: l-selectin; glycoprotein, cell adhesion
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 19756.02

Authors

Wedepohl, S.,Dernedde, J.,Vahedi-Faridi, A.,Tauber, R.,Saenger, W.,Bulut, H. (deposition date: 2017-03-30, release date: 2017-06-14, Last modification date: 2024-10-23)

Primary citation

Wedepohl, S.,Dernedde, J.,Vahedi-Faridi, A.,Tauber, R.,Saenger, W.,Bulut, H.
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

PubMed Abstract: 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 GlcNAc Man N-glycan chain attached to Asn66. Crystal-structure analysis showed that the terminal mannose of GlcNAc Man of one LE010 molecule was coordinated to Ca 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 Ca -binding site reflects the binding mode seen in E- and P-selectin structures co-crystallised with ligands.

PubMed: 28489325
DOI: 10.1002/cbic.201700220

Experimental method

X-RAY DIFFRACTION (1.94 Å)