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- EMDB-70676: Cryo-EM Structure of the Escherichia phage HK446 Rip1 in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70676
TitleCryo-EM Structure of the Escherichia phage HK446 Rip1 in complex with the Enterobacteria phage T6 small terminase
Map data
Sample
  • Complex: Complex of Escherichia phage HK446 Rip1 with Enterobacteria phage T6 small terminase
    • Complex: Enterobacteria phage T6 small terminase
      • Protein or peptide: Small terminase protein
    • Complex: Escherichia phage HK446 Rip1
      • Protein or peptide: ring interacting pore 1 (Rip1)
Keywordsantiphage defence / pore-forming / VIRAL PROTEIN
Function / homologyBacteriophage T4, Gp16, DNA-packaging / Terminase DNA packaging enzyme / Small terminase protein / Uncharacterized protein
Function and homology information
Biological speciesEnterobacteria phage T6 (virus) / Escherichia phage HK446 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPatel PH / Maxwell KL / Norris MJ
Funding support Canada, 5 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-04956 Canada
Canadian Institutes of Health Research (CIHR)PJT-165936 Canada
Canadian Institutes of Health Research (CIHR)FDN-15427 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)SMFSU-581368-2023 Canada
Canada Research ChairsCRC-2023-00010 Canada
CitationJournal: Nature / Year: 2026
Title: A pore-forming antiphage defence is activated by oligomeric phage proteins.
Authors: Pramalkumar H Patel / Matthew R McCarthy / Véronique L Taylor / Gregory B Cole / Chi Zhang / Matthew M Edghill / Landon J Getz / Beatrice C M Fung / Trevor F Moraes / Alan R Davidson / ...Authors: Pramalkumar H Patel / Matthew R McCarthy / Véronique L Taylor / Gregory B Cole / Chi Zhang / Matthew M Edghill / Landon J Getz / Beatrice C M Fung / Trevor F Moraes / Alan R Davidson / Michael J Norris / Karen L Maxwell /
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. Here we describe a 164- ...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. 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.
History
DepositionMay 16, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70676.png

Downloads & links

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Map

FileDownload / File: emd_70676.map.gz / Format: CCP4 / Size: 206 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.0758
Minimum - Maximum-0.16221717 - 0.3924144
Average (Standard dev.)0.00064009323 (±0.009920538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions378378378
Spacing378378378
CellA=B=C: 351.54 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70676_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70676_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70676_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Escherichia phage HK446 Rip1 with Enterobacteria phage...

EntireName: Complex of Escherichia phage HK446 Rip1 with Enterobacteria phage T6 small terminase
Components
  • Complex: Complex of Escherichia phage HK446 Rip1 with Enterobacteria phage T6 small terminase
    • Complex: Enterobacteria phage T6 small terminase
      • Protein or peptide: Small terminase protein
    • Complex: Escherichia phage HK446 Rip1
      • Protein or peptide: ring interacting pore 1 (Rip1)

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Supramolecule #1: Complex of Escherichia phage HK446 Rip1 with Enterobacteria phage...

SupramoleculeName: Complex of Escherichia phage HK446 Rip1 with Enterobacteria phage T6 small terminase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Enterobacteria phage T6 small terminase

SupramoleculeName: Enterobacteria phage T6 small terminase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Enterobacteria phage T6 (virus)

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Supramolecule #3: Escherichia phage HK446 Rip1

SupramoleculeName: Escherichia phage HK446 Rip1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia phage HK446 (virus)

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Macromolecule #1: Small terminase protein

MacromoleculeName: Small terminase protein / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T6 (virus)
Molecular weightTheoretical: 19.235654 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MEGLDINKLL DISDLPGIDG EEIKVYEPLQ LVEVKSNPQN RTPDLEDDYG VVRRNMHFQQ QMLMDAAKIF LETAKNADSP RHMEVFATL MGQMTTTNRE ILKLHKDMKD ITSEQVGTKG AVPTGQMNIQ NATVFMGSPT ELMDEIGDAY EAQEAREKVI N GTTDHHHH HH

UniProtKB: Small terminase protein

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Macromolecule #2: ring interacting pore 1 (Rip1)

MacromoleculeName: ring interacting pore 1 (Rip1) / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage HK446 (virus)
Molecular weightTheoretical: 18.619467 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GMDEKGIISR ITDAVSGAGG ALMSAVGAVK EIQKMQIDYS VKEKTYELVD KLMDAQQQQM SLNELLMISK DKIIELEEKI NRASKWEEE KKNYEMHTPT VATVVYRLKK SANTGQPMHY LCAQCYESSV KSILQYEGFA PPSNHRMRCH RCNASYLFPK S AFSK

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31874
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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