9WW9

Cryo-EM Structure of Parabacteroide phage PD491P1 Capsid

Summary for 9WW9

• Entry DOI: 10.2210/pdb9ww9/pdb
• EMDB information: 66305
• Descriptor: decoration protein, Capsid protein (2 entities in total)
• Functional Keywords: capsid, parabacteroides phage, virus
• Biological source: Parabacteroides phage PD491P1; More
• Total number of polymer chains: 14
• Total formula weight: 353254.89

Authors

Cai, C.,Wang, A.,Shao, Q. (deposition date: 2025-09-23, release date: 2026-06-24)

Primary citation

Cai, C.,Wang, A.,Shao, Q.,Zhang, J.,Wang, Y.,Hu, H.,Yuan, K.,Li, L.,Wang, X.,Fang, Q.,Ma, Y.
Cryo-EM structures of prevalent gut phage PD491P1 uncover extensive disulfide stabilization and distinct structural adaptations.
Structure, 34:942-954.e2, 2026

PubMed Abstract: Bacteriophages play crucial roles in modulating the human gut microbiome, yet structural characterization of prevalent gut phages remains limited. Here, we present high-resolution cryo-EM structures of Parabacteroides phage PD491P1, which is one of the most abundant bacteriophages in the human gut. The structures reveal its mature virion organization, including the capsid, head-to-tail interface, and tail tip regions. Strikingly, PD491P1 exhibits an exceptionally extensive disulfide bond network that covalently stabilizes nearly the entire virion. Unique structural features include an elaborate portal-adaptor-terminator interface and distinctive, upward-pointing and flexible tail fibers with multiple putative host recognition domains. These structural adaptations may enable phage PD491P1 to achieve survival and robust infection in the challenging gut environment. These findings expand our understanding of gut phage structural diversity, reveal mechanistic insights into phage stability and infection, and provide a foundation for future development of phage-based microbiome therapeutics.

PubMed: 42086047
DOI: 10.1016/j.str.2026.04.005

Experimental method

ELECTRON MICROSCOPY (3.2 Å)