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- EMDB-71539: In situ cryoEM structure of bacteriophage P22 portal barrel -

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Basic information

Entry
Database: EMDB / ID: EMD-71539
TitleIn situ cryoEM structure of bacteriophage P22 portal barrel
Map dataIn situ cryoEM structure of bacteriophage P22 portal barrel
Sample
  • Virus: Salmonella phage P22 (virus)
    • Protein or peptide: Portal protein
Keywordsbacteriophage / portal barrel / VIRAL PROTEIN
Function / homologyviral DNA genome packaging, headful / Phage P22-like portal protein / Phage P22-like portal protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / virion assembly / Portal protein
Function and homology information
Biological speciesLederbergvirus P22 / Salmonella phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsYu H / Molineux IJ / Liu J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)110243 United States
CitationJournal: J Mol Biol / Year: 2026
Title: Structural Basis for Bacteriophage P22 Assembly and Infection Initiation.
Authors: Chunyan Wang / Huaxin Yu / Taehyun Park / Ian J Molineux / Jun Liu /
Abstract: Salmonella phage P22 deploys a highly coordinated tail machine to recognize hosts and initiate infection. Here, we present a cryo-EM structure of wild-type P22 that defines how the tail apparatus ...Salmonella phage P22 deploys a highly coordinated tail machine to recognize hosts and initiate infection. Here, we present a cryo-EM structure of wild-type P22 that defines how the tail apparatus assembles onto the capsid and how they interface. Flexible loop residues on both the portal protein gp1 and the capsid protein gp5 undergo pronounced positional shifts and engage multiple partners to accommodate the C12-C5 symmetry mismatch at the portal-capsid interface. The portal protein gp1 forms a distinctive ∼15-nm barrel that projects deep into the capsid interior. Comparison with a mutant lacking the three internal E (ejection) proteins indicates that these proteins reside within the portal-tail lumen in a poorly ordered state, yet are essential for stabilizing the extended portal barrel. We further show how the hub protein gp10 orchestrates the assembly of four distinct particle isomers through its coordinated interactions with portal gp1, adaptor gp4, tailspike gp9, and needle gp26. Finally, cryo-electron tomography reveals that the gp10 hub acts as a structural foundation for the assembly of one E protein into an extracellular channel that breaches the cell surface, with other E proteins forming a genome-translocating trans-envelope conduit.
History
DepositionJun 30, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71539.png

Downloads & links

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Map

FileDownload / File: emd_71539.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ cryoEM structure of bacteriophage P22 portal barrel
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.0163655 - 1.4421582
Average (Standard dev.)0.02231426 (±0.038570117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 478.464 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_71539_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_71539_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Salmonella phage P22

EntireName: Salmonella phage P22 (virus)
Components
  • Virus: Salmonella phage P22 (virus)
    • Protein or peptide: Portal protein

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Supramolecule #1: Salmonella phage P22

SupramoleculeName: Salmonella phage P22 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10754 / Sci species name: Salmonella phage P22 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Lederbergvirus P22
Molecular weightTheoretical: 12.123472 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
SequenceString:
GQQDPAMVQA QGVLLQGQAE LAKAQNQTLS LQIDAAKVEA QNQLNAARIA EIFNNMDLSK QSEFREFLKT VASFQQDRSE DARANAELL LKGDEQTHKQ RMDIANILQS

UniProtKB: Portal 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: 7.6
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 3 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34674
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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