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- PDB-9oox: Cryo-EM Structure of the Escherichia phage HK446 Rip1 in complex ... -

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Basic information

Entry
Database: PDB / ID: 9oox
TitleCryo-EM Structure of the Escherichia phage HK446 Rip1 in complex with the Enterobacteria phage T6 small terminase
Components
  • Small terminase protein
  • ring interacting pore 1 (Rip1)
KeywordsVIRAL PROTEIN / antiphage defence / pore-forming
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPatel, P.H. / Maxwell, K.L. / Norris, M.J.
Funding support Canada, 5items
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, 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.
History
DepositionMay 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small terminase protein
B: Small terminase protein
C: Small terminase protein
D: Small terminase protein
E: Small terminase protein
F: Small terminase protein
G: Small terminase protein
H: Small terminase protein
I: Small terminase protein
J: Small terminase protein
K: Small terminase protein
L: ring interacting pore 1 (Rip1)
M: ring interacting pore 1 (Rip1)
N: ring interacting pore 1 (Rip1)
O: ring interacting pore 1 (Rip1)
P: ring interacting pore 1 (Rip1)
Q: ring interacting pore 1 (Rip1)
R: ring interacting pore 1 (Rip1)
S: ring interacting pore 1 (Rip1)
T: ring interacting pore 1 (Rip1)
U: ring interacting pore 1 (Rip1)
V: ring interacting pore 1 (Rip1)
W: ring interacting pore 1 (Rip1)


Theoretical massNumber of molelcules
Total (without water)435,02623
Polymers435,02623
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Small terminase protein


Mass: 19235.654 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T6 (virus) / Gene: EcT6_00162 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A346FJP3
#2: Protein
ring interacting pore 1 (Rip1)


Mass: 18619.467 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage HK446 (virus) / Gene: HK446_037 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K7P861
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Escherichia phage HK446 Rip1 with Enterobacteria phage T6 small terminaseCOMPLEXall0MULTIPLE SOURCES
2Enterobacteria phage T6 small terminaseCOMPLEX#11RECOMBINANT
3Escherichia phage HK446 Rip1COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Enterobacteria phage T6 (virus)10666
43Escherichia phage HK446 (virus)1147145
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31874 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 141.62 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004420835
ELECTRON MICROSCOPYf_angle_d0.896528008
ELECTRON MICROSCOPYf_chiral_restr0.04743040
ELECTRON MICROSCOPYf_plane_restr0.0083636
ELECTRON MICROSCOPYf_dihedral_angle_d7.38522737

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