Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	High-resolution Cryo-EM Analysis of the Therapeutic Pseudomonas Phage Pa223.
Journal, issue, pages	J Mol Biol, Vol. 437, Issue 21, Page 169386, Year 2025
Publish date	Aug 12, 2025
Authors	Chun-Feng David Hou / Nathan Bellis / Ravi K Lokareddy / Steven Branston / Johnny Reid / Renae Geier / Angela Soriaga / Lucy Sim / Pierre Kyme / Deborah L Birx / Sebastien Lemire / Gino Cingolani /
PubMed Abstract	Cryogenic electron microscopy (cryo-EM) analysis of bacteriophages is a valuable method for deciphering virus composition and conformational plasticity. In this study, we present a high-resolution ...Cryogenic electron microscopy (cryo-EM) analysis of bacteriophages is a valuable method for deciphering virus composition and conformational plasticity. In this study, we present a high-resolution structural atlas of the Pseudomonas virus Pa223, a phage from the Bruynoghevirus genus that has recently been used in clinical cocktails for treating cystic fibrosis and non-cystic fibrosis bronchiectasis, as well as for compassionate care. By combining bioinformatics, proteomics, cryo-EM single particle analysis, and localized reconstruction, we annotated and built atomic models for eight structural polypeptide chains that form the icosahedral capsid and noncontractile tail. We discovered that the Pa223 capsid is decorated by a spike protein with a unique triple-β helix fold that has no structural homologs in the database. The Pa223 tail features six trimeric tail fibers extending upward, similar to but shorter than those found in phage T7. Unlike T7, the Pa223 tail is extended by two head-to-tail adaptors and sealed by a trimeric tail needle, similar to P22-like phages. We identified a protein bound around the outer perimeter of the portal protein, positioned similarly to the ejection protein gp72, which was identified in the Pseudomonas phage DEV, a Litunavirus phage, and a member of the reclassified Schitoviridae family. This structural clue led us to identify the Pa223 ejection proteins gp53, gp54, and gp56, which bioinformatically resemble those of phage T7 more closely than Schitoviridae. Thus, Pa223 contains various structural elements similar to those in P22-like, T7-like, and Litunavirus phages, providing a foundation for understanding the evolution of ejection proteins in Bruynogheviruses.
External links	J Mol Biol / PubMed:40812680 / PubMed Central
Methods	EM (single particle)
Resolution	2.6 - 4.5 Å
Structure data	49882 9nwi EMDB-49882, PDB-9nwi: Pseudomonas phage Pa223 tail (C6 symmetry) Method: EM (single particle) / Resolution: 2.8 Å 49887 9nwm EMDB-49887, PDB-9nwm: Pseudomonas phage Pa223 Portal (C12 symmetry) Method: EM (single particle) / Resolution: 2.6 Å 49902 9nxk EMDB-49902, PDB-9nxk: Pseudomonas phage Pa223 tail fiber Method: EM (single particle) / Resolution: 3.0 Å 49909 9nxo EMDB-49909, PDB-9nxo: Pseudomonas phage Pa223 periplasmic tunnel (pre-ejection, dodecameric assembly) Method: EM (single particle) / Resolution: 3.0 Å 49910 9nxp EMDB-49910, PDB-9nxp: Pseudomonas phage Pa223 tail needle Method: EM (single particle) / Resolution: 4.5 Å 49916 9ny2 EMDB-49916, PDB-9ny2: Pseudomonas phage Pa223 capsid Method: EM (single particle) / Resolution: 2.6 Å 49925 9ny6 EMDB-49925, PDB-9ny6: Pseudomonas phage Pa223 capsid spike Method: EM (single particle) / Resolution: 3.2 Å EMDB-49926: Pseudomonas phage Pa223 full-virion, asymmetric reconstruction, 4 A resolution Method: EM (single particle) / Resolution: 4.0 Å
Source	pseudomonas virus pa223
Keywords	VIRUS / Constituent protein / Structural protein / Phage tail component / Phage assembly