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- PDB-9nwm: Pseudomonas phage Pa223 Portal (C12 symmetry) -

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Basic information

Entry
Database: PDB / ID: 9nwm
TitlePseudomonas phage Pa223 Portal (C12 symmetry)
ComponentsPortal (Connector) protein
KeywordsVIRUS / Constituent protein / Structural protein / Phage tail component
Function / homology: / Phage SU10 portal protein / Portal (Connector) protein
Function and homology information
Biological speciesPseudomonas virus Pa223
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHou, C.F.D. / Cingolani, G. / Lokareddy, K.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM140733 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)OD024978 United States
CitationJournal: J Mol Biol / Year: 2025
Title: High-resolution cryo-EM analysis of the therapeutic Pseudomonas phage Pa223.
Authors: Chun-Feng David Hou / Nathan Bellis / Ravi K Lokareddy / Steven Branston / Johnny Reid / Renae Geier / Angela Soriaga / Lucy Sim / Pierre Kyme / Deborah Birx / Sebastien Lemire / Gino Cingolani /
Abstract: Cryogenic electron microscopy (cryo-EM) analysis of bacteriophages is a valuable method for deciphering virus composition and conformational plasticity. In this study, we present a high-resolution ...Cryogenic electron microscopy (cryo-EM) analysis of bacteriophages is a valuable method for deciphering virus composition and conformational plasticity. In this study, we present a high-resolution structural atlas of the Pseudomonas virus Pa223, a phage from the Bruynoghevirus genus that has recently been used in clinical cocktails for treating cystic fibrosis and non-cystic fibrosis bronchiectasis, as well as for compassionate care. By combining bioinformatics, proteomics, cryo-EM single particle analysis, and localized reconstruction, we annotated and built atomic models for eight structural polypeptide chains that form the icosahedral capsid and noncontractile tail. We discovered that the Pa223 capsid is decorated by a spike protein with a unique triple-β helix fold that has no structural homologs in the database. The Pa223 tail features six trimeric tail fibers extending upward, similar to but shorter than those found in phage T7. Unlike T7, the Pa223 tail is extended by two head-to-tail adaptors and sealed by a trimeric tail needle, similar to P22-like phages. We identified a protein bound around the outer perimeter of the portal protein, positioned similarly to the ejection protein gp72, which was identified in the Pseudomonas phage DEV, a Litunavirus phage, and a member of the reclassified Schitoviridae family. This structural clue led us to identify the Pa223 ejection proteins gp53, gp54, and gp56, which bioinformatically resemble those of phage T7 more closely than Schitoviridae. Thus, Pa223 contains various structural elements similar to those in P22-like, T7-like, and Litunavirus phages, providing a foundation for understanding the evolution of ejection proteins in Bruynogheviruses.
History
DepositionMar 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Aug 6, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
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Revision 1.1Aug 27, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)974,16712
Polymers974,16712
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 (Connector) protein


Mass: 81180.578 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas virus Pa223 / References: UniProt: A0A5P1L2Y5
Has protein modificationY

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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: Pseudomonas virus Pa223 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas virus Pa223
Source (recombinant)Organism: Pseudomonas aeruginosa (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pseudomonas aeruginosa
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: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
4CTFFIND4CTF correction
7Coot0.9model fitting
9PHENIX1.20_4459model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 62000
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46120 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 89.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003861728
ELECTRON MICROSCOPYf_angle_d0.650683388
ELECTRON MICROSCOPYf_chiral_restr0.04369096
ELECTRON MICROSCOPYf_plane_restr0.004611112
ELECTRON MICROSCOPYf_dihedral_angle_d5.0188280

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