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TitleCryo-EM structures of prevalent gut phage PD491P1 uncover extensive disulfide stabilization and distinct structural adaptations.
Journal, issue, pagesStructure, Vol. 34, Issue 6, Page 942-954.e2, Year 2026
Publish dateJun 4, 2026
AuthorsCan Cai / Aohan Wang / Qianqian Shao / Jieqiong Zhang / Yueting Wang / Hongli Hu / Ke Yuan / Lin Li / Xiaofang Wang / Qianglin Fang / Yingfei Ma /
PubMed AbstractBacteriophages 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 ...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.
External linksStructure / PubMed:42086047
MethodsEM (single particle)
Resolution3.2 - 4.5 Å
Structure data

66305

9ww9

EMDB-66305, PDB-9ww9:
Cryo-EM Structure of Parabacteroide phage PD491P1 Capsid
Method: EM (single particle) / Resolution: 3.2 Å

66306

9wwa

EMDB-66306, PDB-9wwa:
Cryo-EM Structure of Parabacteroide phage PD491P1 head-to-tail interface
Method: EM (single particle) / Resolution: 3.2 Å

66307

9wwb

EMDB-66307, PDB-9wwb:
Cryo-EM structure of the tail tip region of Parabacteroide phage PD491P1 (imposed with C6 symmetry)
Method: EM (single particle) / Resolution: 4.1 Å

66308

9wwc

EMDB-66308, PDB-9wwc:
Cryo-EM structure of the tail tip region of Parabacteroide phage PD491P1 (imposed with C3 symmetry)
Method: EM (single particle) / Resolution: 4.5 Å

Source
  • parabacteroides phage pd491p1 (virus)
KeywordsVIRUS / capsid / Parabacteroides phage / VIRAL PROTEIN / neck / tail / Parabacteroide phage / tail tube / hub / distal tail protein

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