7F2P

The head structure of Helicobacter pylori bacteriophage KHP40


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy.

Kamiya, R.Uchiyama, J.Matsuzaki, S.Murata, K.Iwasaki, K.Miyazaki, N.

(2022) Structure 30: 300

  • DOI: https://doi.org/10.1016/j.str.2021.09.001
  • Primary Citation of Related Structures:  
    7DN2, 7DOU, 7F2P

  • 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.


  • Organizational Affiliation

    Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8777, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cement protein gp16124Helicobacter phage KHP40Mutation(s): 0 
UniProt
Find proteins for I7GUT5 (Helicobacter phage KHP40)
Explore I7GUT5 
Go to UniProtKB:  I7GUT5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7GUT5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
KHP40 MCP386Helicobacter phage KHP40Mutation(s): 0 
UniProt
Find proteins for I7HFY0 (Helicobacter phage KHP40)
Explore I7HFY0 
Go to UniProtKB:  I7HFY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7HFY0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan15K18521
Japan Society for the Promotion of Science (JSPS)Japan18K06154

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-06-12
    Changes: Data collection