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- PDB-10lj: C6 Neck assembly of phage Oekolampad (Bas18) -

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Basic information

Entry
Database: PDB / ID: 10lj
TitleC6 Neck assembly of phage Oekolampad (Bas18)
Components
  • Stopper protein gp12
  • Tail protein gp15
  • Terminator protein gp14
KeywordsVIRUS / Bacteriophage / Cryo-EM SPA
Function / homologyProtein of unknown function DUF4128 / Phage tail terminator protein / Phage tail tube protein 3 / Phage tail tube protein, TTP / Tail protein / Major tail protein / Uncharacterized protein
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.83 Å
AuthorsRosheny, K. / Mihnea, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Mol Biol / Year: 2026
Title: A classic fold with a twist: Structural architecture of Dhillonvirus phage Bas18.
Authors: Rosheny Kumaran / Harry McFarlane / Caitlin J Ewenson / Klemens McJarrow-Keller / Alice-Roza Eruera / Mike Strauss / Mihnea Bostina /
Abstract: Although over 15,000 unique phage genomes have been sequenced, many isolates remain uncharacterised and accessible only within individual laboratories. The BASEL (BActeriophage SElection for your ...Although over 15,000 unique phage genomes have been sequenced, many isolates remain uncharacterised and accessible only within individual laboratories. The BASEL (BActeriophage SElection for your Laboratory) collection comprises 106 newly isolated and characterised virulent bacteriophages that infect the laboratory strain Escherichia coli K-12 and provide an open resource for phage biology. Here, we used cryo-electron microscopy (cryo-EM) to determine the structure of Bas18, a Dhillonvirus siphophage from the BASEL collection. Bas18 assembles an icosahedral capsid with T=7(d) triangulation. The asymmetric unit contains seven copies of the major capsid protein (MCP; gp09) and one dimeric decoration protein (gp64) bound at the centre of each hexamer. The MCP adopts the canonical HK97 fold but features a distinct insertion between the A and P domains, which we designate as G and E loop. The neck assembly consists of the portal, adaptor, stopper and terminator. The helical tail is built from hexameric rings of the tail tube protein, and the tail tip consists of the distal tail protein, hub and central fibre. Despite low sequence similarity, the overall architecture of the neck, tail, and tail tip closely resembles that of bacteriophage T1. In contrast, structural protein sequences are highly conserved (85-99% sequence similarity) across Dhillonviruses indicating a conserved virion architecture within this genus. These results expand the structural knowledge of the BASEL collection and provide a detailed architectural framework for Dhillonvirus phages, contributing to a broader understanding of siphophage structural diversity.
History
DepositionJan 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 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: Stopper protein gp12
B: Terminator protein gp14
C: Tail protein gp15


Theoretical massNumber of molelcules
Total (without water)54,0203
Polymers54,0203
Non-polymers00
Water00
1
A: Stopper protein gp12
B: Terminator protein gp14
C: Tail protein gp15
x 6


Theoretical massNumber of molelcules
Total (without water)324,12118
Polymers324,12118
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein Stopper protein gp12


Mass: 13093.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: A0AAE8B7G6
#2: Protein Terminator protein gp14


Mass: 15209.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: A0AAE7VW56
#3: Protein Tail protein gp15


Mass: 25717.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: A0AAE7VXB5
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

ComponentName: Escherichia phage Oekolampad / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage Oekolampad (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Escherichia coli K-12
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 294.15 K

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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: 750 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
4cryoSPARC4.7.1CTF correction
9ISOLDE1.9model refinement
10PHENIX1.21.2_5419model refinement
11Coot0.9.8.8model refinement
15cryoSPARC4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 5.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18058 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building
ID 3D fitting-IDChain-IDSource nameType
11AAlphaFoldin silico model
21BAlphaFoldin silico model
31CAlphaFoldin silico model
RefinementHighest resolution: 5.83 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001394
ELECTRON MICROSCOPYf_angle_d0.498489
ELECTRON MICROSCOPYf_dihedral_angle_d5.75797
ELECTRON MICROSCOPYf_chiral_restr00
ELECTRON MICROSCOPYf_plane_restr0.00297

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