9AXB | pdb_00009axb

Structure of Gp54 from Escherichia phage Bas11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.252 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9AXB

This is version 1.1 of the entry. See complete history

Literature

A bacterial immunity protein directly senses two disparate phage proteins.

Zhang, T.Cepauskas, A.Nadieina, A.Thureau, A.Coppieters 't Wallant, K.Martens, C.Lim, D.C.Garcia-Pino, A.Laub, M.T.

(2024) Nature 635: 728-735

  • DOI: https://doi.org/10.1038/s41586-024-08039-y
  • Primary Citation Related Structures: 
    9AXB, 9ERV

  • PubMed Abstract: 

    Eukaryotic innate immune systems use pattern recognition receptors to sense infection by detecting pathogen-associated molecular patterns, which then triggers an immune response. Bacteria have similarly evolved immunity proteins that sense certain components of their viral predators, known as bacteriophages 1-6 . Although different immunity proteins can recognize different phage-encoded triggers, individual bacterial immunity proteins have been found to sense only a single trigger during infection, suggesting a one-to-one relationship between bacterial pattern recognition receptors and their ligands 7-11 . Here we demonstrate that the antiphage defence protein CapRel SJ46 in Escherichia coli can directly bind and sense two completely unrelated and structurally different proteins using the same sensory domain, with overlapping but distinct interfaces. Our results highlight the notable versatility of an immune sensory domain, which may be a common property of antiphage defence systems that enables them to keep pace with their rapidly evolving viral predators. We found that Bas11 phages harbour both trigger proteins that are sensed by CapRel SJ46 during infection, and we demonstrate that such phages can fully evade CapRel SJ46 defence only when both triggers are mutated. Our work shows how a bacterial immune system that senses more than one trigger can help prevent phages from easily escaping detection, and it may allow the detection of a broader range of phages. More generally, our findings illustrate unexpected multifactorial sensing by bacterial defence systems and complex coevolutionary relationships between them and their phage-encoded triggers.


  • Organizational Affiliation
    • Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 53.83 kDa 
  • Atom Count: 3,245 
  • Modeled Residue Count: 386 
  • Deposited Residue Count: 468 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gp54
A, B, C, D, E
A, B, C, D, E, F
78Escherichia phage JohannLBurckhardtMutation(s): 0 
UniProt
Find proteins for A0AAE7VUR1 (Escherichia phage JohannLBurckhardt)
Explore A0AAE7VUR1 
Go to UniProtKB:  A0AAE7VUR1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAE7VUR1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.252 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50α = 78.54
b = 54.63β = 78.83
c = 54.59γ = 69.88
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references