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- EMDB-75020: ssRNA phage PRR1 virion with 3' gRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-75020
TitlessRNA phage PRR1 virion with 3' gRNA
Map data
Sample
  • Virus: Perrunavirus olsenii
    • Protein or peptide: Coat Protein
    • Protein or peptide: Maturation Protein
    • RNA: 3' gRNA
KeywordsIncP dependent ssRNA phage PRR1 / VIRUS
Biological speciesPerrunavirus olsenii
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsLill ZR / Zhang J
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI156846 United States
National Science Foundation (NSF, United States)MCB-1902392 United States
Other privateexas A&M University T3 United States
Other privateTexas A&M University X-grant United States
Other privateCPT- Texas AgriLife and Texas A&M University United States
CitationJournal: bioRxiv / Year: 2026
Title: Suppressing Transfer of Antibiotic Resistance by a Small RNA Virus.
Authors: Zachary Lill / Jirapat Thongchol / David Solis / Junjie Zhang /
Abstract: The global rise of antimicrobial resistance (AMR) demands innovative strategies to limit the spread of multidrug-resistant bacteria. Conjugative plasmids, particularly those in the incompatibility ...The global rise of antimicrobial resistance (AMR) demands innovative strategies to limit the spread of multidrug-resistant bacteria. Conjugative plasmids, particularly those in the incompatibility group P (IncP), play a central role in disseminating resistance genes across diverse bacterial species via their encoded Type IV secretion systems (T4SS). Here, we characterize the single-stranded RNA bacteriophage (ssRNA phage) PRR1, which selectively targets AMR ESKAPEE pathogens carrying the IncP plasmid RP4, and assess its ability to inhibit conjugation. Using cryo-electron microscopy, we first resolved the mature PRR1 virion at 3.45 Å resolution revealing two phage maturation protein (Mat)-RNA interactions within the 3' untranslated region (UTR) - a conserved interaction (Mat-U1) and a novel interaction (Mat-V1) for ssRNA phages. To characterize the PRR1-RP4 pilus interaction, we performed alanine-scanning mutagenesis and pinpointed four critical TrbC pilin residues (S12, W13, S72, and R77) for infection. Computational modeling revealed that these residues are located near the termini of the pilin at the phage-pilus interface. Notably, native and non-infectious, UV-crosslinked PRR1 were sufficient to block RP4 transfer, indicating conjugation inhibition does not require a complete infection cycle. Finally, combining PRR1 and antibiotic treatment yielded nine unique phage-resistant mutants within T4SS-associated genes on the RP4 plasmid. Eight of these mutants nearly abolished conjugation, while the frameshift mutant retained ~30% of wild-type efficiency, which is pivotal to clarifying the relationship between phage infection and pilus function. Collectively, these results establish ssRNA phages as specific T4SS plasmid targeting agents and underscore their potential to limit horizontal gene transfer in AMR pathogens.
History
DepositionJan 8, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75020.png

Downloads & links

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Map

FileDownload / File: emd_75020.map.gz / Format: CCP4 / Size: 824 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.)
0.85 Å/pix.
x 600 pix.
= 510. Å		0.85 Å/pix.
x 600 pix.
= 510. Å		0.85 Å/pix.
x 600 pix.
= 510. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.22922409 - 0.4713263
Average (Standard dev.)0.0004917301 (±0.026508104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 510.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75020_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75020_half_map_2.map
Projections & Slices
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Sample components

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Entire : Perrunavirus olsenii

EntireName: Perrunavirus olsenii
Components
  • Virus: Perrunavirus olsenii
    • Protein or peptide: Coat Protein
    • Protein or peptide: Maturation Protein
    • RNA: 3' gRNA

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Supramolecule #1: Perrunavirus olsenii

SupramoleculeName: Perrunavirus olsenii / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2 / NCBI-ID: 2845804 / Sci species name: Perrunavirus olsenii / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 2.648 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 292.0 Å / T number (triangulation number): 3

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Macromolecule #1: Maturation Protein

MacromoleculeName: Maturation Protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Perrunavirus olsenii
Molecular weightTheoretical: 45.913219 KDa
SequenceString: GILRQTFSAE NKSDWTPSTG QRMTQTNISS ADVGVEYATI YRGKGRWVWV QHPEGFLFPW RMPSSYTRGH QIIDLTSSTS TITWASPFS KGSGTRTGVP FENLLNRGNW ESFMESRLDM RPLLTYNEMA RNNVAIRLKV GDAKVNLSVF AAEMKRAVTG L ASNFITVV ...String:
GILRQTFSAE NKSDWTPSTG QRMTQTNISS ADVGVEYATI YRGKGRWVWV QHPEGFLFPW RMPSSYTRGH QIIDLTSSTS TITWASPFS KGSGTRTGVP FENLLNRGNW ESFMESRLDM RPLLTYNEMA RNNVAIRLKV GDAKVNLSVF AAEMKRAVTG L ASNFITVV GLYRAVRKGD FKRVASLIKP DPRQKGFSSR DVAGRWLELN YAIIPLLNDI RGGYEYISEN FEKLMTYSVS SN LKTPVPL HYVEDSSSVS MQASGFRGVR TKVHYVIDLP GLREASRVGL INPLLVGWEL VPYSFVIDWL LPVGNMLEAF TAT HGTKFI SGTRTRWCDI DLNGTVRSQY EGYVDWPNSG LSEQPFTGKI YSISRDVLYD YPMVLPYVKN PFSTTHLINA VALI RNLFK R

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Macromolecule #3: Coat Protein

MacromoleculeName: Coat Protein / type: protein_or_peptide / ID: 3 / Number of copies: 178 / Enantiomer: LEVO
Source (natural)Organism: Perrunavirus olsenii
Molecular weightTheoretical: 14.568501 KDa
SequenceString:
AQLQNLVLKD REATPNDHTF VPRDIRDNVG EVVESTGVPI GESRFTISLR KTSNGRYKST LKLVVPVVQS QTVNGIVTPV VVRTSYVTV DFDYDARSTT KERNNFVGMI ADALKADKML VHDTIVNLQG VY

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Macromolecule #2: 3' gRNA

MacromoleculeName: 3' gRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Perrunavirus olsenii
Molecular weightTheoretical: 42.383074 KDa
SequenceString:
CCGGCGACGU UCGAGUUUUC CUAAGAGAAC UUUAAAGUCG UCGGACGGGG UGUUGGAAAC ACCCCUCCCU CACGGGUGGA UGCUUCGGC UAUAAACAGU UCGGGAAGCU ACGCUUCGCU UCCCGGACAU CCA

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (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: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: From ab-initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30437
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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