9V85

Superfolder GFP fused gp38 receptor binding domain of bacteriophage PP01

Summary for 9V85

• Entry DOI: 10.2210/pdb9v85/pdb
• Descriptor: Green fluorescent protein,Receptor-recognizing protein gp38, CALCIUM ION (3 entities in total)
• Functional Keywords: phage host recognition, phage tail fiber, receptor binding protein, cell adhesion
• Biological source: Aequorea victoria; More
• Total number of polymer chains: 2
• Total formula weight: 101121.57

Authors

Kanamaru, S.,Otsuka, Y. (deposition date: 2025-05-29, release date: 2026-01-07, Last modification date: 2026-02-25)

Primary citation

Terasaki, H.,Zdravkovic, A.,Niwa, T.,Washizaki, A.,Kawaguchi, M.,Yonesaki, T.,Kanamaru, S.,Otsuka, Y.
Structural and functional insights into the interaction between a PP01 phage gp38 tail fiber tip and an Escherichia coli OmpC receptor.
Mbio, 17:-, 2026

PubMed Abstract: Bacteriophages exhibit strict host specificity, primarily determined by adsorption to bacterial surface receptors. However, the molecular basis underlying this specificity remains incompletely understood. Here, we investigate the interaction between outer membrane protein C (OmpC) of O157 and gp38, the receptor-binding protein located at the tip of the long tail fibers of phage PP01. We determined the crystal structure of the receptor-binding domain (RBD) of gp38 at 2.1 Å resolution. The structure reveals a lattice of poly-glycine type II helices with protruding receptor recognition loops, resembling that of gp38 from phage S16. To identify interaction sites, we performed site-specific photo-crosslinking using -benzoyl-L-phenylalanine (pBPA), followed by liquid chromatography-tandem mass spectrometry. Two critical contacts were identified: Gly208 in loop-D of gp38 crosslinked to Ser225 and Pro226 in extracellular loop-5 of OmpC, and Tyr230 in loop-E of gp38 to the Val304-Arg308 region in loop-7 of OmpC. A structural model of the gp38-OmpC complex was constructed using distance-constrained prediction and validated by targeted mutagenesis. Our findings demonstrate that PP01 phage specificity is governed by loop-E of gp38 engaging a cleft formed by loops -5 and -7 of OmpC. These structural and functional insights enhance our understanding of phage-host recognition and may inform the rational design of engineered bacteriophages with altered host ranges.IMPORTANCEBacteriophages must precisely recognize and bind to specific molecules on the surface of their bacterial hosts to initiate infection, but the details of these interactions are often unclear. In this study, we examined how phage PP01 targets O157. Using structural analysis of the phage tail fiber and a technique to capture contact points between the phage and a bacterial surface protein, we mapped the molecular basis of host recognition. We also developed a simple test system using a modified phage to identify which parts of the tail fiber are essential for binding. These methods can be broadly applied to other phages to better understand how they select their hosts. This work provides valuable insights and tools that could aid the design of phages with customized host specificity for therapeutic or biotechnological applications.

PubMed: 41511108
DOI: 10.1128/mbio.02110-25

Experimental method

X-RAY DIFFRACTION (2.1 Å)