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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: Patel PH / McCarthy MR / Taylor VL / Cole GB / Zhang C / Edghill MM / Getz LJ / Fung BCM / Moraes TF / Davidson AR / Norris MJ / Maxwell KL
History
DepositionMay 16, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 378 pix.
= 351.54 Å		0.93 Å/pix.
x 378 pix.
= 351.54 Å		0.93 Å/pix.
x 378 pix.
= 351.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
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

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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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