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- PDB-9pdp: In situ cryoEM structure of bacteriophage P22 portal barrel -

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Basic information

Entry
Database: PDB / ID: 9pdp
TitleIn situ cryoEM structure of bacteriophage P22 portal barrel
ComponentsPortal protein
KeywordsVIRAL PROTEIN / bacteriophage / portal barrel
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsYu, H. / Molineux, I.J. / Liu, J.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein


Theoretical massNumber of molelcules
Total (without water)145,48212
Polymers145,48212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Portal protein / Gene product 1 / Gp1 / Head-to-tail connector


Mass: 12123.472 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lederbergvirus P22
Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P26744
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Salmonella phage P22 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Salmonella phage P22 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Salmonella enterica subsp. enterica serovar Typhimurium
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1600 nm / Calibrated defocus max: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5190model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34674 / Symmetry type: POINT

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