9JHT | pdb_00009jht

Jumbo phage Killer B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 
    0.268 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Jumbo phage killer immune system targets early infection of nucleus-forming phages.

Yuping, L.Guan, L.Becher, I.Makarova, K.S.Cao, X.Hareendranath, S.Guan, J.Stein, F.Yang, S.Boergel, A.Lapouge, K.Remans, K.Agard, D.Savitski, M.Typas, A.Koonin, E.V.Feng, Y.Bondy-Denomy, J.

(2025) Cell 188: 2127-2140.e21

  • DOI: https://doi.org/10.1016/j.cell.2025.02.016
  • Primary Citation of Related Structures:  
    9JHT

  • PubMed Abstract: 

    Jumbo bacteriophages of the ϕKZ-like family assemble a lipid-based early phage infection (EPI) vesicle and a proteinaceous nucleus-like structure during infection. These structures protect the phage from nucleases and may create selective pressure for immunity mechanisms targeting this specific phage family. Here, we identify "jumbo phage killer" (Juk), a two-component immune system that terminates infection of ϕKZ-like phages, suppressing the expression of early phage genes and preventing phage DNA replication and phage nucleus assembly while saving the cell. JukA (formerly YaaW) rapidly senses the EPI vesicle by binding to an early-expressed phage protein, gp241, and then directly recruits JukB. The JukB effector structurally resembles a pore-forming toxin and destabilizes the EPI vesicle. Functional anti-ϕKZ JukA homologs are found across bacterial phyla, associated with diverse effectors. These findings reveal a widespread defense system that specifically targets early events executed by ϕKZ-like jumbo phages prior to phage nucleus assembly.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA. Electronic address: yuping.li@unibas.ch.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
JukB
A, B
335Shewanella xiamenensisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.268 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.26α = 90
b = 98.85β = 90
c = 199.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references