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- EMDB-74964: Icosahedral Capsid assembly of phage Oekolampad (Bas18) -

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Basic information

Entry
Database: EMDB / ID: EMD-74964
TitleIcosahedral Capsid assembly of phage Oekolampad (Bas18)
Map dataIcosahedral Capsid assembly of phage Oekolampad (Bas18)
Sample
  • Virus: Escherichia phage Oekolampad (virus)
    • Protein or peptide: Major capsid protein gp09
    • Protein or peptide: Decoration protein gp64
KeywordsBacteriophage / Cryo-EM SPA / VIRUS
Function / homologyMajor capsid protein 13-like / Major capsid protein 13-like / Uncharacterized protein / Major capsid protein
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia phage Oekolampad (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRosheny K / Harry M / Mike S / Mihnea B
Funding support1 items
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 6, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74964.png

Downloads & links

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Map

FileDownload / File: emd_74964.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral Capsid assembly of phage Oekolampad (Bas18)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 1280 pix.
= 1094.4 Å		0.86 Å/pix.
x 1280 pix.
= 1094.4 Å		0.86 Å/pix.
x 1280 pix.
= 1094.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0051
Minimum - Maximum-0.010414753 - 0.02269045
Average (Standard dev.)0.00014979212 (±0.0013627103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128012801280
Spacing128012801280
CellA=B=C: 1094.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_74964_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_74964_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage Oekolampad

EntireName: Escherichia phage Oekolampad (virus)
Components
  • Virus: Escherichia phage Oekolampad (virus)
    • Protein or peptide: Major capsid protein gp09
    • Protein or peptide: Decoration protein gp64

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Supramolecule #1: Escherichia phage Oekolampad

SupramoleculeName: Escherichia phage Oekolampad / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Escherichia phage Oekolampad was propagated in Escherichia coli K-12
NCBI-ID: 2851982 / Sci species name: Escherichia phage Oekolampad / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli K-12 (bacteria)
Virus shellShell ID: 1 / T number (triangulation number): 7

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Macromolecule #1: Major capsid protein gp09

MacromoleculeName: Major capsid protein gp09 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 38.479785 KDa
SequenceString: MSLTVFQRKL VTAVTQMIPD NLNVFNAAAN GAVVLGTGEV LKDVIEKMSV GLIANLVTDR NAYAPVGTPA TAKVLARMLT NSVNLSAKV GPVAITKAMM AKIETNVNSV AAEIAAQATQ AIMLHYLKAG IGASKAAIES NAAAKYTQPA RVDGVGGRTF P TLADFPLA ...String:
MSLTVFQRKL VTAVTQMIPD NLNVFNAAAN GAVVLGTGEV LKDVIEKMSV GLIANLVTDR NAYAPVGTPA TAKVLARMLT NSVNLSAKV GPVAITKAMM AKIETNVNSV AAEIAAQATQ AIMLHYLKAG IGASKAAIES NAAAKYTQPA RVDGVGGRTF P TLADFPLA ASKFGDQASL IKSWFMDGVT WANFIAYQAL PSAEQVFAIG DLQVMGDGLG RRFIISDAAA DAMGAGNMLG LV PGAVAVT TNGLDMLAQE KGGNENIERW WQGEFDFNVA VKGYRLKASA RTPIEGVRSF KLSDITTKDN WELDQGQVDN APA TVQDVG AVGDGDTKGR RKTQAAQEVP TRHIKETAGV LVTLTATTAS

UniProtKB: Major capsid protein

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Macromolecule #2: Decoration protein gp64

MacromoleculeName: Decoration protein gp64 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 5.590318 KDa
SequenceString:
MLKSILDHNA DALAALAKTE DPGARAIIAD TISHAGIFDA KLPSPPPPEE PGPAA

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: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 294.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 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: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 25695
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9zys:
Icosahedral Capsid assembly of phage Oekolampad (Bas18)

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