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- EMDB-68938: Tail tip assembly of phage Oekolampad (Bas18) -

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Basic information

Entry
Database: EMDB / ID: EMD-68938
TitleTail tip assembly of phage Oekolampad (Bas18)
Map data
Sample
  • Virus: Escherichia phage Oekolampad (virus)
    • Protein or peptide: Tail protein gp15
    • Protein or peptide: Distal tail protein gp20
    • Protein or peptide: Hub protein gp21
    • Protein or peptide: J-like tail tip protein gp24
KeywordsBacteriophage / Cryo-EM SPA / E.coli / VIRUS
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.82 Å
AuthorsKumaran R / Bostina M
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
DepositionFeb 5, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68938.png

Downloads & links

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Map

FileDownload / File: emd_68938.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. 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: 0.221
Minimum - Maximum-0.4240508 - 0.7622593
Average (Standard dev.)0.0029618272 (±0.047980897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68938_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68938_half_map_2.map
Projections & Slices
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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: Tail protein gp15
    • Protein or peptide: Distal tail protein gp20
    • Protein or peptide: Hub protein gp21
    • Protein or peptide: J-like tail tip protein gp24

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Supramolecule #1: Escherichia phage Oekolampad

SupramoleculeName: Escherichia phage Oekolampad / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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: Tail protein gp15

MacromoleculeName: Tail protein gp15 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Oekolampad (virus)
Molecular weightTheoretical: 25.717959 KDa
SequenceString: MGYQLPNGSS VQIGSVLGSG IAVTAATNAA ASISDLTQGC VITCAASHGL VVGDVVMFTK TPWVRALNRA FIVGKVDTND VTLARFDTE DVTKYPTGAF SVGTPGEVVK VSGFIDFPFI TNVAVSGGDQ QTTTFQPLQV NTAISLNTTK NPLVQTYTFT H DEEDPIRP ...String:
MGYQLPNGSS VQIGSVLGSG IAVTAATNAA ASISDLTQGC VITCAASHGL VVGDVVMFTK TPWVRALNRA FIVGKVDTND VTLARFDTE DVTKYPTGAF SVGTPGEVVK VSGFIDFPFI TNVAVSGGDQ QTTTFQPLQV NTAISLNTTK NPLVQTYTFT H DEEDPIRP ILEDLDDTQK TTVIKFTNPA AASGKGEIRI YPAKVSFQKI PSAEVNNVET VQSTLTMQSD MVIYRKDLVE AL S

UniProtKB: Major tail protein

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Macromolecule #2: Distal tail protein gp20

MacromoleculeName: Distal tail protein gp20 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Oekolampad (virus)
Molecular weightTheoretical: 21.815311 KDa
SequenceString: MSQGTITLTK GSKTITGVGT AFLSEIGKVR VFTHIDGNDY TGKIAEFNSN TVITLADNWA GPTKAGAAYE LIEAHDPRSN EWPYYWHMQ LQGGGDVQLA FRSEELQFGN GYGQNIADGP NAETKQFPVQ FIGLTTDKWC NPKLVYNFLR GHFVKPFVVT A PDGETGLF ...String:
MSQGTITLTK GSKTITGVGT AFLSEIGKVR VFTHIDGNDY TGKIAEFNSN TVITLADNWA GPTKAGAAYE LIEAHDPRSN EWPYYWHMQ LQGGGDVQLA FRSEELQFGN GYGQNIADGP NAETKQFPVQ FIGLTTDKWC NPKLVYNFLR GHFVKPFVVT A PDGETGLF VVERSSLSYT DNGHYTATVS ATLKTAIGFV R

UniProtKB: Minor tail protein

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Macromolecule #3: Hub protein gp21

MacromoleculeName: Hub protein gp21 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Oekolampad (virus)
Molecular weightTheoretical: 28.87049 KDa
SequenceString: MNKLYREATR FDPSGRVRLI HIDAQDVEPG DGAIGAGHHY FHYCFIPHTA EDIAAAGGDE DKLKPKSIFF GGQEFEFWPF DLSGLNFST STAAEPQLTI VDIGGIITRL SLNHDQLLGA KVEIIDTFAK FLDNGTDPDP TQKRVQEYYI DSQVGRNPGK Q ITFALSSP ...String:
MNKLYREATR FDPSGRVRLI HIDAQDVEPG DGAIGAGHHY FHYCFIPHTA EDIAAAGGDE DKLKPKSIFF GGQEFEFWPF DLSGLNFST STAAEPQLTI VDIGGIITRL SLNHDQLLGA KVEIIDTFAK FLDNGTDPDP TQKRVQEYYI DSQVGRNPGK Q ITFALSSP ADMEGQVVPR RQIMNMCEWA LNGKYASGDG CTWNLAKPGI KYYDERGNEV IAMNMDRCGG CLSDCYLRFG QG LADPKAA VLDFGGFPGS RLIKG

UniProtKB: Minor tail protein

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Macromolecule #4: J-like tail tip protein gp24

MacromoleculeName: J-like tail tip protein gp24 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Oekolampad (virus)
Molecular weightTheoretical: 126.604594 KDa
SequenceString: MTIIYDVTGH KGGGGKQHTP QETPDSLHSL AKIRILLALG EGEFESITSA SELRQRVYLD GTPIQNADLS ENFPGARVEF RPGTQHQDV IHGFSAVESE QSVGVKLENG TPWVRQINDT SLDAVRIRIG IPALYTNEDN GDLVGGRIDY KIVVYTDNAD P REFRFAAV ...String:
MTIIYDVTGH KGGGGKQHTP QETPDSLHSL AKIRILLALG EGEFESITSA SELRQRVYLD GTPIQNADLS ENFPGARVEF RPGTQHQDV IHGFSAVESE QSVGVKLENG TPWVRQINDT SLDAVRIRIG IPALYTNEDN GDLVGGRIDY KIVVYTDNAD P REFRFAAV GKTMSLYERD HRIELPPNVN TGWRVEVHRI TADSTSAKVV NDIQVQSITE IIDARLRYPL TALLFVEFDA KA FQNIPRV SIKCKGRKVL VPNNYDPINH TYSGDWDGTF KRAWTDNPAW HWYDICITER FGLGRRIKPQ MLNRYALYQI AQR CDQLVS DGNGGREIRF KNDMYIQSQT DAWTVLKDLA AIFAGMTWWG NQMLNIVSDQ PVAAVSHTIT NASVIDGRFD YASG SQKTR YSTFAVAYGN PKNHYEDAIA TGQRVELVRR HKINRLDITA IGCTRESEAQ RRGHWALISN QLDQQVSFKV GMEGL FFIP GSVVAIADTN ISGGFETRGG RLLSDPGTRT VLNTDSEITF RPGDKFLVRT DSGNVETREI ASVNGNKVTL KTALDA DPI PDQPFCVDGN DIQLQKFRIT DLEYDDSTST FSVRGIEYND SKYDAVDNGA RLDPGIFTQV PDGVMKGPES VTITPSQ IS SQGQLITNVD IVFPPVKDAV VYEIQWRRTS LQNMAVQWGN DWVNIPRTAS NGAHIPNVFS GNYQARVRAI GMGEISSP W VSSAITPVEG RLGGLNAPII TNAISGLHQI LWKWNHNNAA TDISYTELEV RKTGETEWKF LTNVPYPGAE YAQTSLEFG IYQQLRARVA DKIGNLSDWS DPFEGQVSDN VDEYMKGLDD EFLTSEDGKR FQEAIDTMPQ GIYEAMLTDA QQLFNARAEY KGIYAEISV AYNVAADAHQ AVAQLETLIG TRLDDAEAAI HTLQTAQSTQ EQAFAQYQQT VAAKFSEQEA AIQSVQTATA D VAGALAEY KTQVAAQFGQ QSAAIEQKMT SSFNHSGGSA TYSLKAGVTY NGTYYDAGMQ LSVVTSGSAV KSRIAFKADQ FY IMHPSNG TLSSAFIVDG GTVYIDTARI KNASINFAQI TDTLQSNNFA SGSRGWRIWK GGAAEFNEVT VRGNLYATSG NFG FSGGTV TIDKTGVNVP LPGGGRVKVG TW

UniProtKB: J-like tail tip 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 BIOCONTINUUM (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: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 4342
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial model
ChainDetails
chain_id: A, source_name: AlphaFold, initial_model_type: in silico modelThe alphafold model was refined into the map
chain_id: B, source_name: AlphaFold, initial_model_type: in silico modelThe alphafold model was refined into the map
chain_id: C, source_name: SwissModel, initial_model_type: in silico modelThe model was rigid body fitted into the map
chain_id: D, source_name: SwissModel, initial_model_type: in silico modelThe model was rigid body fitted into the map and residues with no map density was deleted
RefinementProtocol: FLEXIBLE FIT
Output model

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

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