PDBsum entry 4hep

Viral protein

PDB id: 4hep

Contents

Protein chains

162 a.a.

130 a.a.

Ligands

SO4

Waters ×325

References listed in PDB file

Key reference

• Title: Viral infection modulation and neutralization by camelid nanobodies.
• Authors: A.Desmyter, C.Farenc, J.Mahony, S.Spinelli, C.Bebeacua, S.Blangy, D.Veesler, D.Van sinderen, C.Cambillau.
• Ref.: Proc Natl Acad Sci U S A, 2013, 110, E1371. [DOI no: 10.1073/pnas.1301336110]
• PubMed id: 23530214

Abstract

Lactococcal phages belong to a large family of Siphoviridae and infect Lactococcus lactis, a gram-positive bacterium used in commercial dairy fermentations. These phages are believed to recognize and bind specifically to pellicle polysaccharides covering the entire bacterium. The phage TP901-1 baseplate, located at the tip of the tail, harbors 18 trimeric receptor binding proteins (RBPs) promoting adhesion to a specific lactococcal strain. Phage TP901-1 adhesion does not require major conformational changes or Ca(2+), which contrasts other lactococcal phages. Here, we produced and characterized llama nanobodies raised against the purified baseplate and the Tal protein of phage TP901-1 as tools to dissect the molecular determinants of phage TP901-1 infection. Using a set of complementary techniques, surface plasmon resonance, EM, and X-ray crystallography in a hybrid approach, we identified binders to the three components of the baseplate, analyzed their affinity for their targets, and determined their epitopes as well as their functional impact on TP901-1 phage infectivity. We determined the X-ray structures of three nanobodies in complex with the RBP. Two of them bind to the saccharide binding site of the RBP and are able to fully neutralize TP901-1 phage infectivity, even after 15 passages. These results provide clear evidence for a practical use of nanobodies in circumventing lactococcal phages viral infection in dairy fermentation.