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- PDB-9pgg: Cryo-EM structure of bacteriophage P22 gp1-gp5-gp4 complex at 2.7... -

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Basic information

Entry
Database: PDB / ID: 9pgg
TitleCryo-EM structure of bacteriophage P22 gp1-gp5-gp4 complex at 2.76 angstrom
Components
  • Major capsid protein
  • Peptidoglycan hydrolase gp4
  • Portal protein
KeywordsVIRAL PROTEIN / Phage capsid-tail interface
Function / homology
Function and homology information


viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral procapsid / viral portal complex / viral procapsid maturation / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / virus tail / T=7 icosahedral viral capsid ...viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral procapsid / viral portal complex / viral procapsid maturation / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / virus tail / T=7 icosahedral viral capsid / virion assembly / viral capsid / hydrolase activity / identical protein binding
Similarity search - Function
Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / Major capsid protein Gp5 / P22 coat protein - gene protein 5
Similarity search - Domain/homology
Portal protein / Head-to-tail adapter protein gp4 / Major capsid protein
Similarity search - Component
Biological speciesSalmonella phage P22 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsYu, H. / Liu, J. / Molienux, I.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110243 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
DepositionJul 7, 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

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Assembly

Deposited unit
Aa: Major capsid protein
Ab: Major capsid protein
Ac: Major capsid protein
Ad: Major capsid protein
Ae: Major capsid protein
Af: Major capsid protein
Ag: Major capsid protein
Ah: Major capsid protein
Ai: Major capsid protein
Aj: Major capsid protein
Ak: Major capsid protein
Al: Major capsid protein
Am: Major capsid protein
An: Major capsid protein
Ao: Major capsid protein
Ap: Peptidoglycan hydrolase gp4
Aq: Peptidoglycan hydrolase gp4
Ar: Peptidoglycan hydrolase gp4
As: Peptidoglycan hydrolase gp4
At: Peptidoglycan hydrolase gp4
Au: Peptidoglycan hydrolase gp4
Av: Peptidoglycan hydrolase gp4
Aw: Peptidoglycan hydrolase gp4
Ax: Peptidoglycan hydrolase gp4
Ay: Peptidoglycan hydrolase gp4
Az: Peptidoglycan hydrolase gp4
Ba: Peptidoglycan hydrolase gp4
Bb: Portal protein
Bd: Portal protein
Bf: Portal protein
Bh: Portal protein
Bj: Portal protein
Bl: Portal protein
Bn: Portal protein
Bp: Portal protein
Br: Portal protein
Bt: Portal protein
Bv: Portal protein
Bx: Portal protein


Theoretical massNumber of molelcules
Total (without water)1,912,42639
Polymers1,912,42639
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
Major capsid protein


Mass: 46795.613 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage P22 (virus) / Production host: Salmonella enterica (bacteria) / References: UniProt: P26747
#2: Protein
Peptidoglycan hydrolase gp4


Mass: 18044.959 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage P22 (virus) / Production host: Salmonella enterica (bacteria) / References: UniProt: P26746
#3: Protein
Portal protein / Gene product 1 / Gp1 / Head-to-tail connector


Mass: 82829.375 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage P22 (virus) / Production host: Salmonella enterica (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 weightExperimental value: NO
Source (natural)Organism: Salmonella phage P22 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Salmonella enterica
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 1200 nm / Nominal defocus min: 600 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
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 177125
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93834 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 56.75 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003122415
ELECTRON MICROSCOPYf_angle_d0.6113166177
ELECTRON MICROSCOPYf_chiral_restr0.043518411
ELECTRON MICROSCOPYf_plane_restr0.004621966
ELECTRON MICROSCOPYf_dihedral_angle_d6.977816994

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