PDBsum entry 4k5u

Immune system

PDB id: 4k5u

Contents

Protein chains

218 a.a.

Ligands

GAL ×4

Waters ×384

PDB id:

4k5u

Name:

Immune system

Title:

Recognition of the bg-h antigen by a lamprey variable lymphocyte receptor

Structure:

Variable lymphocyte receptor. Chain: b, a, c, d. Engineered: yes

Source:

Petromyzon marinus. Marine lamprey. Organism_taxid: 7757. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.206 R-free: 0.247

Authors:

M.Luo,C.A.Velikovsky,X.B.Yang,R.A.Mariuzza

Key ref:

M.Luo et al. (2013). Recognition of the Thomsen-Friedenreich pancarcinoma carbohydrate antigen by a lamprey variable lymphocyte receptor. J Biol Chem, 288, 23597-23606. PubMed id: 23782692 DOI: 10.1074/jbc.M113.480467

Date:

15-Apr-13 Release date: 26-Jun-13

Protein chains

K0IE77  (K0IE77_PETMA) -  Variable lymphocyte receptor (Fragment) from Petromyzon marinus

Seq: 219 a.a.

Struc: 218 a.a.

DOI no: 10.1074/jbc.M113.480467

J Biol Chem 288:23597-23606 (2013)

PubMed id: 23782692

Recognition of the Thomsen-Friedenreich pancarcinoma carbohydrate antigen by a lamprey variable lymphocyte receptor.

M.Luo, C.A.Velikovsky, X.Yang, M.A.Siddiqui, X.Hong, J.J.Barchi, J.C.Gildersleeve, Z.Pancer, R.A.Mariuzza.

ABSTRACT

Variable lymphocyte receptors (VLRs) are leucine-rich repeat proteins that mediate adaptive immunity in jawless vertebrates. VLRs were recently shown to recognize glycans, such as the tumor-associated Thomsen-Friedenreich antigen (TFα; Galβ1-3GalNAcα), with a selectivity rivaling or exceeding that of lectins and antibodies. To understand the basis for TFα recognition by one such VLR (VLRB.aGPA.23), we measured thermodynamic parameters for the binding interaction and determined the structure of the VLRB.aGPA.23-TFα complex to 2.2 Å resolution. In the structure, four tryptophan residues form a tight hydrophobic cage encasing the TFα disaccharide that completely excludes buried water molecules. This cage together with hydrogen bonding of sugar hydroxyls to polar side chains explains the exquisite selectivity of VLRB.aGPA.23. The topology of the glycan-binding site of VLRB.aGPA.23 differs markedly from those of lectins or antibodies, which typically consist of long, convex grooves for accommodating the oligosaccharide. Instead, the TFα disaccharide is sandwiched between a variable loop and the concave surface of the VLR formed by the β-strands of the leucine-rich repeat modules. Longer oligosaccharides are predicted to extend perpendicularly across the β-strands, requiring them to bend to match the concavity of the VLR solenoid.