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- PDB-23gd: Tail tip assembly of phage Oekolampad (Bas18) -

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Basic information

Entry
Database: PDB / ID: 23gd
TitleTail tip assembly of phage Oekolampad (Bas18)
Components
  • Distal tail protein gp20
  • Hub protein gp21
  • J-like tail tip protein gp24
  • Tail protein gp15
KeywordsVIRUS / Bacteriophage / Cryo-EM SPA / E.coli
Function / homology
Function and homology information


iron-sulfur cluster binding / host cell cytoplasm / symbiont entry into host cell
Similarity search - Function
Phage tail tube protein 3 / Phage tail tube protein, TTP / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Phage minor tail protein L / Phage minor tail protein / : / Tip attachment protein J,FNIII-A domain / : / Domain of unknown function DUF1983 ...Phage tail tube protein 3 / Phage tail tube protein, TTP / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Phage minor tail protein L / Phage minor tail protein / : / Tip attachment protein J,FNIII-A domain / : / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Tip attachment protein J / Putative phage tail protein
Similarity search - Domain/homology
Minor tail protein / Minor tail protein / Major tail protein / J-like tail tip protein
Similarity search - Component
Biological speciesEscherichia phage Oekolampad (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.82 Å
AuthorsKumaran, R. / Bostina, M.
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
DepositionFeb 5, 2026Deposition site: PDBJ / Processing site: PDBJ
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

Downloads & links

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Assembly

Deposited unit
A: Tail protein gp15
B: Distal tail protein gp20
C: Hub protein gp21
D: J-like tail tip protein gp24
E: Tail protein gp15
F: Distal tail protein gp20


Theoretical massNumber of molelcules
Total (without water)250,5426
Polymers250,5426
Non-polymers00
Water00
1
A: Tail protein gp15
B: Distal tail protein gp20
C: Hub protein gp21
D: J-like tail tip protein gp24
E: Tail protein gp15
F: Distal tail protein gp20

A: Tail protein gp15
B: Distal tail protein gp20
C: Hub protein gp21
D: J-like tail tip protein gp24
E: Tail protein gp15
F: Distal tail protein gp20

A: Tail protein gp15
B: Distal tail protein gp20
C: Hub protein gp21
D: J-like tail tip protein gp24
E: Tail protein gp15
F: Distal tail protein gp20


Theoretical massNumber of molelcules
Total (without water)751,62518
Polymers751,62518
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
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: C3 (3 fold cyclic))

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Components

#1: Protein Tail protein gp15 / Tail tube protein gp15


Mass: 25717.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Oekolampad (virus) / References: UniProt: A0AAE7VXB5
#2: Protein Distal tail protein gp20 / Distal tail protein gp20


Mass: 21815.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Oekolampad (virus) / References: UniProt: A0AAE7VX38
#3: Protein Hub protein gp21 / Hub protein gp21


Mass: 28870.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Oekolampad (virus) / References: UniProt: A0AAE7VW64
#4: Protein J-like tail tip protein gp24 / Central fibre protein gp24


Mass: 126604.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Oekolampad (virus) / References: UniProt: A0AAE8B1D2
Has protein modificationY

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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
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia phage Oekolampad (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Escherichia coli K-12
Virus shellTriangulation number (T number): 7
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 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
12cryoSPARC4.7.13D reconstruction
13ISOLDE1.8model refinement
14PHENIX1.21.2_5419model refinement
15Coot0.9.8.8model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 7.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4342 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building
ID 3D fitting-IDChain-IDDetails (eV)Source nameType
11AThe alphafold model was refined into the mapAlphaFoldin silico model
21BThe alphafold model was refined into the mapAlphaFoldin silico model
31CThe model was rigid body fitted into the mapSwissModelin silico model
41DThe model was rigid body fitted into the map and residues with no map density was deletedSwissModelin silico model

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