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- EMDB-72290: Asymmetric reconstruction of filled phage capsids with broken tails -

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Basic information

Entry
Database: EMDB / ID: EMD-72290
TitleAsymmetric reconstruction of filled phage capsids with broken tails
Map data
Sample
  • Virus: Oshimavirus P7426
Keywordsbacteriophage / thermophilic / neck / portal / VIRUS
Biological speciesOshimavirus P7426
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsSedivy EL / Agnello EA / Song K / Xu C / Kelch BA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817338 United States
CitationJournal: J Mol Biol / Year: 2026
Title: The structure of a thermostable phage's portal vertex and neck complex illuminates the headful maturation mechanism.
Authors: Emma L Sedivy / Emily Agnello / Julia E Hobaugh / Rakeyah Ahsan / Kangkang Song / Chen Xu / Brian A Kelch /
Abstract: Viruses assemble from component parts inside their host cells, but the mechanisms coordinating this complex process are not completely understood. In tailed bacteriophages, the genome is packaged ...Viruses assemble from component parts inside their host cells, but the mechanisms coordinating this complex process are not completely understood. In tailed bacteriophages, the genome is packaged into its capsid shell through the portal complex. The portal complex then closes to retain DNA and connects to the tail, which is required for host recognition and infection. The trigger to stop pumping DNA and assemble the mature virus has been a longstanding conundrum in the field. We determined the structure of the portal, the proteins that connect it to the tail, and portal vertex in the hyperthermophilic phage Oshimavirus using cryo-Electron Microscopy (cryo-EM). We find highly intertwined loop structures, like in a wicker basket, potentially stabilizing the portal vertex against high temperatures. Moreover, we observe that the portal protrudes from the capsid in mature virions. We propose that portal is repositioned by packaged DNA, forming a pressure-sensitive switch that terminates genome packaging and triggers tail attachment in headful phages.
History
DepositionAug 22, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72290.png

Downloads & links

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Map

FileDownload / File: emd_72290.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.64 Å/pix.
x 512 pix.
= 1349.46 Å		2.64 Å/pix.
x 512 pix.
= 1349.46 Å		2.64 Å/pix.
x 512 pix.
= 1349.46 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.63566 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.8446028 - 2.348834
Average (Standard dev.)-0.0048831427 (±0.15668592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1349.46 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72290_msk_1.map
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Half map: #1

Fileemd_72290_half_map_1.map
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Half map: #2

Fileemd_72290_half_map_2.map
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Sample components

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Entire : Oshimavirus P7426

EntireName: Oshimavirus P7426
Components
  • Virus: Oshimavirus P7426

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Supramolecule #1: Oshimavirus P7426

SupramoleculeName: Oshimavirus P7426 / type: virus / ID: 1 / Parent: 0
Details: Virions with broken tails were purified from infected Thermus thermophilus using cesium chloride gradient centrifugation. Virions with broken tails migrate in a band lower in the gradient ...Details: Virions with broken tails were purified from infected Thermus thermophilus using cesium chloride gradient centrifugation. Virions with broken tails migrate in a band lower in the gradient (more dense) than mature virions.
NCBI-ID: 466052 / Sci species name: Oshimavirus P7426 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Virus shellShell ID: 1 / Name: Capsid / Diameter: 820.0 Å / T number (triangulation number): 7

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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: 8
GridModel: EMS Lacey Carbon / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1814 / Average electron dose: 49.2668 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 79000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: Local Refinement / Number images used: 13186
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: Local Refinement
FSC plot (resolution estimation)

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