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- EMDB-72288: dsDNA in the central channel of the bacteriophage P74-26 neck -

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Basic information

Entry
Database: EMDB / ID: EMD-72288
TitledsDNA in the central channel of the bacteriophage P74-26 neck
Map data
Sample
  • Virus: Oshimavirus P7426
    • DNA: DNA (66-MER)
    • DNA: DNA (66-MER)
Keywordsbacteriophage / thermophilic / Neck / Portal / VIRUS / VIRUS-DNA complex
Biological speciesOshimavirus P7426
Methodsingle particle reconstruction / cryo EM / Resolution: 4.54 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
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_72288.png

Downloads & links

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Map

FileDownload / File: emd_72288.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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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.44495785 - 0.9391107
Average (Standard dev.)-0.007503806 (±0.055281915)
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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Additional map: #1

Fileemd_72288_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_72288_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_72288_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
    • DNA: DNA (66-MER)
    • DNA: DNA (66-MER)

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Supramolecule #1: Oshimavirus P7426

SupramoleculeName: Oshimavirus P7426 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Virions were purified from infected Thermus thermophilus using cesium chloride 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
Virus shellShell ID: 1 / Name: capsid / Diameter: 820.0 Å / T number (triangulation number): 7

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Macromolecule #1: DNA (66-MER)

MacromoleculeName: DNA (66-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 20.091855 KDa
SequenceString: (DA)(DC)(DC)(DC)(DA)(DC)(DA)(DT)(DC)(DA) (DG)(DC)(DC)(DC)(DA)(DC)(DA)(DC)(DG)(DC) (DA)(DG)(DG)(DG)(DG)(DA)(DG)(DA)(DA) (DA)(DA)(DT)(DT)(DC)(DT)(DG)(DC)(DT)(DG) (DT) (DC)(DC)(DT)(DT)(DC)(DG) ...String:
(DA)(DC)(DC)(DC)(DA)(DC)(DA)(DT)(DC)(DA) (DG)(DC)(DC)(DC)(DA)(DC)(DA)(DC)(DG)(DC) (DA)(DG)(DG)(DG)(DG)(DA)(DG)(DA)(DA) (DA)(DA)(DT)(DT)(DC)(DT)(DG)(DC)(DT)(DG) (DT) (DC)(DC)(DT)(DT)(DC)(DG)(DC)(DC) (DA)(DG)(DT)(DT)(DG)(DC)(DA)(DT)(DC)(DT) (DC)(DT) (DA)(DC)(DC)(DT)(DC)(DC)

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Macromolecule #2: DNA (66-MER)

MacromoleculeName: DNA (66-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 20.603148 KDa
SequenceString: (DG)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DA)(DG) (DA)(DT)(DG)(DC)(DA)(DA)(DC)(DT)(DG)(DG) (DC)(DG)(DA)(DA)(DG)(DG)(DA)(DC)(DA) (DG)(DC)(DA)(DG)(DA)(DA)(DT)(DT)(DT)(DT) (DC) (DT)(DC)(DC)(DC)(DC)(DT) ...String:
(DG)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DA)(DG) (DA)(DT)(DG)(DC)(DA)(DA)(DC)(DT)(DG)(DG) (DC)(DG)(DA)(DA)(DG)(DG)(DA)(DC)(DA) (DG)(DC)(DA)(DG)(DA)(DA)(DT)(DT)(DT)(DT) (DC) (DT)(DC)(DC)(DC)(DC)(DT)(DG)(DC) (DG)(DT)(DG)(DT)(DG)(DG)(DG)(DC)(DT)(DG) (DA)(DT) (DG)(DT)(DG)(DG)(DG)(DT)

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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 / 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 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: Local Refinement
Details: FSC was calculated inside the provided mask, which only covers the lumen of the Neck channel
Number images used: 19306
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. 4.6.2) / Software - details: Local Refinement
Final 3D classificationNumber classes: 10 / Avg.num./class: 38000 / Software - Name: cryoSPARC (ver. 4.6.2) / Software - details: 3D Classification
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
SoftwareName: Coot
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9q7a:
dsDNA in the central channel of the bacteriophage P74-26 neck

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