9K3N image
Deposition Date 2024-10-19
Release Date 2025-08-13
Last Version Date 2025-08-20
Entry Detail
PDB ID:
9K3N
Keywords:
VIRUS
Title:
The structure of Salmonella phage PJNS002
Biological Source:
Source Organism:
Salmonella phage PJNS002 (Taxon ID: 3377957)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.59 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9K3N validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*AP*AP*AP*A)-3')
Chain IDs:D (auth: A), I (auth: E), N (auth: L), S (auth: P), X (auth: T), CA (auth: Y), HA (auth: CA), MA (auth: GA), RA (auth: KA), WA (auth: OA), BB (auth: SA), GB (auth: WA), LB (auth: AB), QB (auth: EB), VB (auth: IB), AC (auth: MB), FC (auth: QB), KC (auth: UB), PC (auth: YB), UC (auth: CC), ZC (auth: GC), ED (auth: KC), JD (auth: OC), OD (auth: SC), TD (auth: WC), YD (auth: AD), DE (auth: ED), IE (auth: ID), NE (auth: MD), SE (auth: QD), XE (auth: UD), CF (auth: YD), HF (auth: CE), MF (auth: GE), RF (auth: KE), WF (auth: OE), BG (auth: SE), GG (auth: WE), LG (auth: AF), QG (auth: EF), VG (auth: IF), AH (auth: MF), FH (auth: QF), KH (auth: UF), PH (auth: YF), UH (auth: CG), ZH (auth: GG), EI (auth: KG), JI (auth: OG), OI (auth: SG), TI (auth: WG), YI (auth: AH), DJ (auth: EH), IJ (auth: IH), NJ (auth: MH), SJ (auth: QH), XJ (auth: UH), CK (auth: YH), HK (auth: CI), MK (auth: GI)
Chain Length:4
Number of Molecules:60
Biological Source:Salmonella phage PJNS002
Polymer Type:polypeptide(L)
Molecule:capsid protein F
Chain IDs:A (auth: F), F (auth: B), K (auth: H), P (auth: M), U (auth: Q), Z (auth: V), EA (auth: Z), JA (auth: DA), OA (auth: HA), TA (auth: LA), YA (auth: PA), DB (auth: TA), IB (auth: XA), NB (auth: BB), SB (auth: FB), XB (auth: JB), CC (auth: NB), HC (auth: RB), MC (auth: VB), RC (auth: ZB), WC (auth: DC), BD (auth: HC), GD (auth: LC), LD (auth: PC), QD (auth: TC), VD (auth: XC), AE (auth: BD), FE (auth: FD), KE (auth: JD), PE (auth: ND), UE (auth: RD), ZE (auth: VD), EF (auth: ZD), JF (auth: DE), OF (auth: HE), TF (auth: LE), YF (auth: PE), DG (auth: TE), IG (auth: XE), NG (auth: BF), SG (auth: FF), XG (auth: JF), CH (auth: NF), HH (auth: RF), MH (auth: VF), RH (auth: ZF), WH (auth: DG), BI (auth: HG), GI (auth: LG), LI (auth: PG), QI (auth: TG), VI (auth: XG), AJ (auth: BH), FJ (auth: FH), KJ (auth: JH), PJ (auth: NH), UJ (auth: RH), ZJ (auth: VH), EK (auth: ZH), JK (auth: DI)
Chain Length:4
Number of Molecules:60
Biological Source:Salmonella phage PJNS002
Polymer Type:polypeptide(L)
Molecule:spike protein G
Chain IDs:B (auth: G), G (auth: C), L (auth: I), Q (auth: N), V (auth: R), AA (auth: W), FA (auth: AA), KA (auth: EA), PA (auth: IA), UA (auth: MA), ZA (auth: QA), EB (auth: UA), JB (auth: YA), OB (auth: CB), TB (auth: GB), YB (auth: KB), DC (auth: OB), IC (auth: SB), NC (auth: WB), SC (auth: AC), XC (auth: EC), CD (auth: IC), HD (auth: MC), MD (auth: QC), RD (auth: UC), WD (auth: YC), BE (auth: CD), GE (auth: GD), LE (auth: KD), QE (auth: OD), VE (auth: SD), AF (auth: WD), FF (auth: AE), KF (auth: EE), PF (auth: IE), UF (auth: ME), ZF (auth: QE), EG (auth: UE), JG (auth: YE), OG (auth: CF), TG (auth: GF), YG (auth: KF), DH (auth: OF), IH (auth: SF), NH (auth: WF), SH (auth: AG), XH (auth: EG), CI (auth: IG), HI (auth: MG), MI (auth: QG), RI (auth: UG), WI (auth: YG), BJ (auth: CH), GJ (auth: GH), LJ (auth: KH), QJ (auth: OH), VJ (auth: SH), AK (auth: WH), FK (auth: AI), KK (auth: EI)
Chain Length:177
Number of Molecules:60
Biological Source:Salmonella phage PJNS002
Polymer Type:polypeptide(L)
Molecule:DNA-binding protein J
Chain IDs:C (auth: J), H (auth: D), M (auth: K), R (auth: O), W (auth: S), BA (auth: X), GA (auth: BA), LA (auth: FA), QA (auth: JA), VA (auth: NA), AB (auth: RA), FB (auth: VA), KB (auth: ZA), PB (auth: DB), UB (auth: HB), ZB (auth: LB), EC (auth: PB), JC (auth: TB), OC (auth: XB), TC (auth: BC), YC (auth: FC), DD (auth: JC), ID (auth: NC), ND (auth: RC), SD (auth: VC), XD (auth: ZC), CE (auth: DD), HE (auth: HD), ME (auth: LD), RE (auth: PD), WE (auth: TD), BF (auth: XD), GF (auth: BE), LF (auth: FE), QF (auth: JE), VF (auth: NE), AG (auth: RE), FG (auth: VE), KG (auth: ZE), PG (auth: DF), UG (auth: HF), ZG (auth: LF), EH (auth: PF), JH (auth: TF), OH (auth: XF), TH (auth: BG), YH (auth: FG), DI (auth: JG), II (auth: NG), NI (auth: RG), SI (auth: VG), XI (auth: ZG), CJ (auth: DH), HJ (auth: HH), MJ (auth: LH), RJ (auth: PH), WJ (auth: TH), BK (auth: XH), GK (auth: BI), LK (auth: FI)
Chain Length:4
Number of Molecules:60
Biological Source:Salmonella phage PJNS002
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*AP*AP*AP*A)-3')
Chain IDs:E (auth: U), J (auth: a), O (auth: b), T (auth: c), Y (auth: d), DA (auth: e), IA (auth: f), NA (auth: g), SA (auth: h), XA (auth: i), CB (auth: j), HB (auth: k), MB (auth: l), RB (auth: m), WB (auth: n), BC (auth: o), GC (auth: p), LC (auth: q), QC (auth: r), VC (auth: s), AD (auth: t), FD (auth: u), KD (auth: v), PD (auth: w), UD (auth: x), ZD (auth: y), EE (auth: z), JE (auth: 0), OE (auth: 1), TE (auth: 2), YE (auth: 3), DF (auth: 4), IF (auth: 5), NF (auth: 6), SF (auth: 7), XF (auth: 8), CG (auth: 9), HG (auth: aA), MG (auth: bA), RG (auth: cA), WG (auth: dA), BH (auth: eA), GH (auth: fA), LH (auth: gA), QH (auth: hA), VH (auth: iA), AI (auth: jA), FI (auth: kA), KI (auth: lA), PI (auth: mA), UI (auth: nA), ZI (auth: oA), EJ (auth: pA), JJ (auth: qA), OJ (auth: rA), TJ (auth: sA), YJ (auth: tA), DK (auth: uA), IK (auth: vA), NK (auth: wA)
Chain Length:4
Number of Molecules:60
Biological Source:Salmonella phage PJNS002
Ligand Molecules
NA
Primary Citation
Structural basis for Salmonella infection by two Microviridae phages.
Commun Biol 8 1166 1166 (2025)
PMID: 40770068 DOI: 10.1038/s42003-025-08595-7

Abstact

The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage therapy. Microviridae phages offer a promising model for studying phage-host interactions with their unique structural and infection mechanisms. Here, we identify two Microviridae phages, PJNS001 and PJNS002, with different host receptor dependencies, and determine their cryo-EM structures at 2.68 Å and 2.59 Å resolution, respectively. These icosahedral capsids with T = 1 symmetry exhibit a unique vertex reinforcement mechanism, stabilizing the viral assembly. The specific pentameric adaptations, coupled with DNA binding protein engagements and thermodynamic constraints, collectively preclude the formation of hybrid virions. Structural analysis and in situ visualization reveal spike protein features and host-attachment intermediates, informing host specificity. Together, these findings advance our understanding of Microviridae infection mechanisms and provide a structural framework for rational phage design against antibiotic-resistant pathogens.

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Primary Citation of related structures
9K3N