9OOX | pdb_00009oox

Cryo-EM Structure of the Escherichia phage HK446 Rip1 in complex with the Enterobacteria phage T6 small terminase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

A pore-forming antiphage defence is activated by oligomeric phage proteins.

Patel, P.H.McCarthy, M.R.Taylor, V.L.Cole, G.B.Zhang, C.Edghill, M.M.Getz, L.J.Fung, B.C.M.Moraes, T.F.Davidson, A.R.Norris, M.J.Maxwell, K.L.

(2026) Nature 651: 1060-1067

  • DOI: https://doi.org/10.1038/s41586-025-10075-1
  • Primary Citation Related Structures: 
    9OOX

  • PubMed Abstract: 

    Bacteria have evolved a wide array of defence systems to combat phage infection, many of which rely on complex signalling systems and large protein complexes to function 1 . Here we describe a 164-residue prophage-encoded protein that defends bacteria by sensing conserved oligomeric components of phage assembly. This protein, called ring interacting pore 1 (Rip1), is activated by the portal or small terminase proteins of infecting phages-oligomeric ring-shaped complexes that are essential for virion maturation. Rip1 uses these phage protein ring complexes as a template to assemble into membrane-disrupting pores that inhibit phage virion assembly and cause premature death of the host cell. Rip1 homologues are widely distributed across bacteria and provide robust defence against diverse phages. This study reveals a strategy by which a small defence protein integrates both sensing and effector activity by exploiting a conserved feature of viral assembly. The mechanism mirrors eukaryotic pore-forming immunity but is executed by a single protein, offering an evolutionarily streamlined solution to viral detection and defence.


  • Organizational Affiliation
    • Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 435.03 kDa 
  • Atom Count: 20,448 
  • Modeled Residue Count: 2,513 
  • Deposited Residue Count: 3,838 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Small terminase protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K
170Enterobacteria phage T6Mutation(s): 0 
Gene Names: EcT6_00162
UniProt
Find proteins for A0A346FJP3 (Enterobacteria phage T6)
Explore A0A346FJP3 
Go to UniProtKB:  A0A346FJP3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A346FJP3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ring interacting pore 1 (Rip1)
L, M, N, O, P
L, M, N, O, P, Q, R, S, T, U, V, W
164Escherichia phage HK446Mutation(s): 0 
Gene Names: HK446_037
UniProt
Find proteins for K7P861 (Escherichia phage HK446)
Explore K7P861 
Go to UniProtKB:  K7P861
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7P861
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2023-04956
Canadian Institutes of Health Research (CIHR)CanadaPJT-165936
Canadian Institutes of Health Research (CIHR)CanadaFDN-15427
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaSMFSU-581368-2023
Canada Research ChairsCanadaCRC-2023-00010

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Data collection, Database references
  • Version 1.2: 2026-04-01
    Changes: Data collection, Database references