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- EMDB-70283: C12 reconstruction of the thermophilic bacteriophage P74-26 Neck -

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Basic information

Entry
Database: EMDB / ID: EMD-70283
TitleC12 reconstruction of the thermophilic bacteriophage P74-26 Neck
Map data
Sample
  • Virus: Oshimavirus P7426
    • Complex: Neck
Keywordsbacteriophage / thermophilic / Neck / Portal / VIRUS
Biological speciesOshimavirus P7426
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsSedivy EL / Agnello E / 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
DepositionApr 21, 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_70283.png

Downloads & links

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Map

FileDownload / File: emd_70283.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.42763636 - 1.1044
Average (Standard dev.)-0.00375074 (±0.058648508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70283_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_70283_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_70283_half_map_2.map
Projections & Slices
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Sample components

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Entire : Oshimavirus P7426

EntireName: Oshimavirus P7426
Components
  • Virus: Oshimavirus P7426
    • Complex: Neck

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Supramolecule #1: Oshimavirus P7426

SupramoleculeName: Oshimavirus P7426 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Virions were purified from infected Thermus thermophilus using cesium chloride and sucrose gradient ultracentrifugation.
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

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Supramolecule #2: Neck

SupramoleculeName: Neck / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Oshimavirus P7426

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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: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
DetailsVirions were purified from infected Thermus thermophilus using cesium chloride and sucrose gradient ultracentrifugation.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16184 / Average electron dose: 49.0571 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware:
Namedetails
cryoSPARC (ver. 4.1.0)Patch CTF Estimation
cryoSPARC (ver. 4.4.1)Local CTF Refinement

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Non-Uniform Refinement
Details: FSC was calculated using the provided mask, which excludes the capsid and its contents (C5) as well as the tail tube (C3).
Number images used: 31671
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Non-Uniform Refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Initial model was created by ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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