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- EMDB-49887: Pseudomonas phage Pa223 Portal (C12 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-49887
TitlePseudomonas phage Pa223 Portal (C12 symmetry)
Map data
Sample
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Portal (Connector) protein
KeywordsConstituent protein / Structural protein / Phage tail component / VIRUS
Function / homology: / Phage SU10 portal protein / Portal (Connector) 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 24, 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_49887.png

Downloads & links

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Map

FileDownload / File: emd_49887.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.022100182 - 0.06907636
Average (Standard dev.)0.0043493137 (±0.004161331)
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_49887_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_49887_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_49887_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: Portal (Connector) 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: Portal (Connector) protein

MacromoleculeName: Portal (Connector) protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa223
Molecular weightTheoretical: 81.180578 KDa
SequenceString: MAKRRRKIKP MDDEQVLRHL DQLVNDALDF NSSELSKQRS EALKYYFGEP FGNERPGKSA IVSRDVQETV DWIMPSLMKV FTSGGQVVK YEPQTAEDVE QAEQETEYVN YLFMRKNEGF KVMFDWFQDT LMMKTGVVKV YVEEVLNPTF ERFSGLSEEM V ADILADPD ...String:
MAKRRRKIKP MDDEQVLRHL DQLVNDALDF NSSELSKQRS EALKYYFGEP FGNERPGKSA IVSRDVQETV DWIMPSLMKV FTSGGQVVK YEPQTAEDVE QAEQETEYVN YLFMRKNEGF KVMFDWFQDT LMMKTGVVKV YVEEVLNPTF ERFSGLSEEM V ADILADPD TEILAQSVDE DGTYSIKIRK DKKKREIKVT CIKPENFLVD RLATCIDDAR FLCHREKYTV SDLRLLGVPE DV LDELPYD EYEFSDSQPE RLVRDNFDMT GQLQYNSGDD AEANREVWAS ECYTLLDVDG DGISELRRIL YVGDYIISNE PWD CRPFAD LNAYRIAHKF HGMSVYDKIR DIQEIRSVLM RNIMDNIYRT NQGRSVVLDG QVNLEDLLTN EAAGIVRVKA MNSI MPLET PQLSGEVYGM LDRLEADRGK RTGITDRTRG LDQNTLHSNQ AAMSVNQLMT AAEQQIDLIA RMFAETGVKR LFQLL HDHA IKYQNQEEVF QLRGKWVAIN PANWRERSDL TVTVGIGNMN KDQQMLHLMR IWEMAQAVVG GGGLGVLVSE QNLYNI LKE VTENAGYKDP DRFWTNPDSP EAQQAKAIRE QKEAQPKPED IKAQADAQRA QSDALAKQAE AQMKQVEAQI RLAEIEL KK QEAVLQQREM ALKEAELQLE RDRFTWERAR NEAEYHLEAT QARAAYIGDG KVPETKKPSK AVRK

UniProtKB: Portal (Connector) 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: 46120
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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