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- EMDB-49916: Pseudomonas phage Pa223 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-49916
TitlePseudomonas phage Pa223 capsid
Map data
Sample
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Capsid and scaffold protein
KeywordsConstituent protein / Structural protein / Phage tail component / VIRUS
Function / homologyProtein of unknown function DUF5309 / SU10 major capsid protein / Capsid and scaffold protein
Function and homology information
Biological speciesPseudomonas virus Pa223
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHou CFD / Cingolani G / Lokareddy KR
Funding support United States, 3 items
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 L 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 26, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49916.png

Downloads & links

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Map

FileDownload / File: emd_49916.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 512 pix.
= 484.352 Å		0.95 Å/pix.
x 512 pix.
= 484.352 Å		0.95 Å/pix.
x 512 pix.
= 484.352 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0046532485 - 0.11288423
Average (Standard dev.)0.012482251 (±0.00714856)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 484.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49916_msk_1.map
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Half map: #1

Fileemd_49916_half_map_1.map
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Half map: #2

Fileemd_49916_half_map_2.map
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Sample components

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Entire : Pseudomonas virus Pa223

EntireName: Pseudomonas virus Pa223
Components
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Capsid and scaffold protein

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Supramolecule #1: Pseudomonas virus Pa223

SupramoleculeName: Pseudomonas virus Pa223 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2590840 / Sci species name: Pseudomonas virus Pa223 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Capsid and scaffold protein

MacromoleculeName: Capsid and scaffold protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa223
Molecular weightTheoretical: 35.053477 KDa
SequenceString: MATPTNAVST VEINGKREDL IDIIYNIAPY DTPFMTAIGK GVATAITHEW QTDELRQPGK NTRVEGEDAT IKAGSFTTML NNFCQISDE TLQVTGTADK VKKAGRKNEL AYQLAKKSKE LKLDMEYAMV GAPQAKIQRN TTTPGQMANI FAYYKTNGSV G ANGTLPTG ...String:
MATPTNAVST VEINGKREDL IDIIYNIAPY DTPFMTAIGK GVATAITHEW QTDELRQPGK NTRVEGEDAT IKAGSFTTML NNFCQISDE TLQVTGTADK VKKAGRKNEL AYQLAKKSKE LKLDMEYAMV GAPQAKIQRN TTTPGQMANI FAYYKTNGSV G ANGTLPTG DGSDTGTAGD LRLLTEDMLL NASEAIWRNG GQANSIQTSS SIKKAISKNM KGRATEITLD ASDNRIAQTV DV YESDFGK YTIRANRWFH ENTMFIFDPK MHALCYLRPF FQHELAKTGD SEKRQLLVEY TLRVNNEKSG ALIRDVVAQV

UniProtKB: Capsid and scaffold 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 62000
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 46000 / Random conical tilt - Tilt angle: 15 degrees
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144000
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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