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- PDB-9zzy: ssRNA phage PRR1 virion with 3' gRNA -

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Basic information

Entry
Database: PDB / ID: 9zzy
TitlessRNA phage PRR1 virion with 3' gRNA
Components
  • 3' gRNA
  • Coat Protein
  • Maturation Protein
KeywordsVIRUS / IncP dependent ssRNA phage PRR1
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesPerrunavirus olsenii
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsLill, Z.R. / Zhang, J.
Funding support United States, 5items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 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

Downloads & links

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Assembly

Deposited unit
F: Maturation Protein
AE: 3' gRNA
0: Coat Protein
1: Coat Protein
2: Coat Protein
3: Coat Protein
4: Coat Protein
5: Coat Protein
6: Coat Protein
7: Coat Protein
8: Coat Protein
9: Coat Protein
A: Coat Protein
B: Coat Protein
C: Coat Protein
D: Coat Protein
E: Coat Protein
O: Coat Protein
P: Coat Protein
Q: Coat Protein
R: Coat Protein
S: Coat Protein
T: Coat Protein
U: Coat Protein
V: Coat Protein
W: Coat Protein
X: Coat Protein
Y: Coat Protein
Z: Coat Protein
a: Coat Protein
b: Coat Protein
c: Coat Protein
d: Coat Protein
e: Coat Protein
f: Coat Protein
g: Coat Protein
h: Coat Protein
i: Coat Protein
j: Coat Protein
k: Coat Protein
l: Coat Protein
m: Coat Protein
n: Coat Protein
o: Coat Protein
p: Coat Protein
q: Coat Protein
r: Coat Protein
s: Coat Protein
t: Coat Protein
u: Coat Protein
v: Coat Protein
w: Coat Protein
x: Coat Protein
y: Coat Protein
z: Coat Protein
G: Coat Protein
H: Coat Protein
I: Coat Protein
J: Coat Protein
K: Coat Protein
L: Coat Protein
M: Coat Protein
N: Coat Protein
AA: Coat Protein
AB: Coat Protein
AC: Coat Protein
AD: Coat Protein
AO: Coat Protein
AP: Coat Protein
AQ: Coat Protein
AR: Coat Protein
AS: Coat Protein
AT: Coat Protein
AU: Coat Protein
AV: Coat Protein
AW: Coat Protein
AX: Coat Protein
AY: Coat Protein
AZ: Coat Protein
Aa: Coat Protein
Ab: Coat Protein
Ac: Coat Protein
Ad: Coat Protein
Ae: Coat Protein
Af: Coat Protein
Ag: Coat Protein
Ah: Coat Protein
Ai: Coat Protein
Aj: Coat Protein
Ak: Coat Protein
Al: Coat Protein
Am: Coat Protein
An: Coat Protein
Ao: Coat Protein
Ap: Coat Protein
Aq: Coat Protein
Ar: Coat Protein
As: Coat Protein
At: Coat Protein
Au: Coat Protein
Av: Coat Protein
Aw: Coat Protein
Ax: Coat Protein
Ay: Coat Protein
Az: Coat Protein
A1: Coat Protein
A2: Coat Protein
A3: Coat Protein
A4: Coat Protein
A5: Coat Protein
A6: Coat Protein
A7: Coat Protein
A8: Coat Protein
A9: Coat Protein
A0: Coat Protein
BA: Coat Protein
BB: Coat Protein
BC: Coat Protein
BD: Coat Protein
BE: Coat Protein
BF: Coat Protein
BG: Coat Protein
BH: Coat Protein
BI: Coat Protein
BJ: Coat Protein
BK: Coat Protein
BL: Coat Protein
BM: Coat Protein
BN: Coat Protein
BO: Coat Protein
BP: Coat Protein
BQ: Coat Protein
BR: Coat Protein
BS: Coat Protein
BV: Coat Protein
BY: Coat Protein
BZ: Coat Protein
Bb: Coat Protein
Bc: Coat Protein
Bd: Coat Protein
Bg: Coat Protein
Bh: Coat Protein
Bi: Coat Protein
Bj: Coat Protein
Bk: Coat Protein
Bl: Coat Protein
Bm: Coat Protein
Bn: Coat Protein
Bu: Coat Protein
Bv: Coat Protein
Bw: Coat Protein
Bx: Coat Protein
By: Coat Protein
Bz: Coat Protein
B1: Coat Protein
B2: Coat Protein
B3: Coat Protein
B4: Coat Protein
B5: Coat Protein
B6: Coat Protein
B7: Coat Protein
B8: Coat Protein
B9: Coat Protein
B0: Coat Protein
CA: Coat Protein
CB: Coat Protein
CC: Coat Protein
CD: Coat Protein
CH: Coat Protein
CI: Coat Protein
CK: Coat Protein
CL: Coat Protein
CM: Coat Protein
CN: Coat Protein
CO: Coat Protein
CP: Coat Protein
CQ: Coat Protein
CR: Coat Protein
CS: Coat Protein
CT: Coat Protein


Theoretical massNumber of molelcules
Total (without water)2,681,489180
Polymers2,681,489180
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 Maturation Protein


Mass: 45913.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perrunavirus olsenii
#2: RNA chain 3' gRNA


Mass: 42383.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Perrunavirus olsenii
#3: Protein ...
Coat Protein


Mass: 14568.501 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Source: (natural) Perrunavirus olsenii
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: Perrunavirus olsenii / Type: VIRUS / Entity ID: #3, #1-#2 / Source: NATURAL
Molecular weightValue: 2.648 MDa / Experimental value: NO
Source (natural)Organism: Perrunavirus olsenii
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pseudomonas aeruginosa / Strain: PAO1
Virus shellName: Capsid / Diameter: 292 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.8
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: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
4cryoSPARCCTF correction
12cryoSPARC3D reconstruction
13PHENIX1.21.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30437 / Symmetry type: POINT

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