7DN2

Acidic stable capsid structure of Helicobacter pylori bacteriophage KHP30

Summary for 7DN2

• Entry DOI: 10.2210/pdb7dn2/pdb
• EMDB information: 30778
• Descriptor: Major structural protein ORF14, Cement protein gp15 (2 entities in total)
• Functional Keywords: capsid, phage, phage head, cryoem, virus
• Biological source: Helicobacter pylori bacteriophage KHP30; More
• Total number of polymer chains: 18
• Total formula weight: 505686.45

Authors

Kamiya, R.,Uchiyama, J.,Matsuzaki, S.,Murata, K.,Iwasaki, K.,Miyazaki, N. (deposition date: 2020-12-08, release date: 2021-10-27, Last modification date: 2024-05-29)

Primary citation

Kamiya, R.,Uchiyama, J.,Matsuzaki, S.,Murata, K.,Iwasaki, K.,Miyazaki, N.
Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy.
Structure, 30:300-, 2022

PubMed Abstract: The acid-stable capsid structures of Helicobacter pylori phages KHP30 and KHP40 are solved at 2.7 and 3.0 Å resolutions by cryoelectron microscopy, respectively. The capsids have icosahedral T = 9 symmetry and consist of each 540 copies of 2 structural proteins, a major capsid protein, and a cement protein. The major capsid proteins form 12 pentagonal capsomeres occupying icosahedral vertexes and 80 hexagonal capsomeres located at icosahedral faces and edges. The major capsid protein has a unique protruding loop extending to the neighboring subunit that stabilizes hexagonal capsomeres. Furthermore, the capsid is decorated with trimeric cement proteins with a jelly roll motif. The cement protein trimer sits on the quasi-three-fold axis formed by three major capsid protein capsomeres, thereby enhancing the particle stability by connecting these capsomeres. Sequence and structure comparisons between the related Helicobacter pylori phages suggest a possible mechanism of phage adaptation to the human gastric environment.

PubMed: 34597601
DOI: 10.1016/j.str.2021.09.001

Experimental method

ELECTRON MICROSCOPY (2.7 Å)