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- EMDB-62023: The structure of Salmonella phage PJNS002 -

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Basic information

Entry
Database: EMDB / ID: EMD-62023
TitleThe structure of Salmonella phage PJNS002
Map data
SampleMicroviridae != Salmonella phage PJNS002

Microviridae

  • Virus: Salmonella phage PJNS002 (virus)
    • Protein or peptide: capsid protein F
    • Protein or peptide: spike protein G
    • Protein or peptide: DNA-binding protein J
  • DNA: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
  • DNA: DNA (5'-D(P*AP*AP*AP*A)-3')
Keywordsstructual proteins / VIRUS
Biological speciesSalmonella phage PJNS002 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsHu WL / Chen YB / Wei YM / Gao Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other government23QA1406400 China
CitationJournal: Commun Biol / Year: 2025
Title: Structural basis for Salmonella infection by two Microviridae phages.
Authors: Wanlong Hu / Zhengjie Liu / Yuming Wei / Qucheng Bian / Weiqi Lan / Chongzheng Fan / Jiaoyang Song / Qianqian Sun / Xiaojie Zhang / Yuqing Liu / Yan Gao / Yibao Chen /
Abstract: 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 ...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.
History
DepositionOct 19, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62023.png

Downloads & links

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Map

FileDownload / File: emd_62023.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-2.4476821 - 4.0398765
Average (Standard dev.)0.03618706 (±0.25521976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62023_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62023_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Microviridae

EntireName: Microviridae (isometric ssDNA phages)
Components
  • Virus: Salmonella phage PJNS002 (virus)
    • Protein or peptide: capsid protein F
    • Protein or peptide: spike protein G
    • Protein or peptide: DNA-binding protein J
  • DNA: DNA (5'-D(P*AP*AP*AP*AP*A)-3')
  • DNA: DNA (5'-D(P*AP*AP*AP*A)-3')

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Supramolecule #1: Salmonella phage PJNS002

SupramoleculeName: Salmonella phage PJNS002 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: T=1 icosahedral virus / NCBI-ID: 10841 / Sci species name: Salmonella phage PJNS002 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Salmonella (bacteria)
Molecular weightTheoretical: 4.31 MDa
Virus shellShell ID: 1 / Diameter: 290.0 Å / T number (triangulation number): 1

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Macromolecule #1: capsid protein F

MacromoleculeName: capsid protein F / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage PJNS002 (virus)
Molecular weightTheoretical: 48.418332 KDa
SequenceString: MSNVQTSAQR DRIDLSHLGF LSGQIGRLKT VSFSPVIAGD SFELDAVGAL RLSPLRRGLA IDSNVDYFTF YIPYRHVYGQ TWIDFMKDG VNATPLPTVT TGIDMDQTAY LGTVNPTSGI MPKFLHQSYL NIYNNYFKAP WMPDRTEANP SNLNDADSRY G FRCCHLKT ...String:
MSNVQTSAQR DRIDLSHLGF LSGQIGRLKT VSFSPVIAGD SFELDAVGAL RLSPLRRGLA IDSNVDYFTF YIPYRHVYGQ TWIDFMKDG VNATPLPTVT TGIDMDQTAY LGTVNPTSGI MPKFLHQSYL NIYNNYFKAP WMPDRTEANP SNLNDADSRY G FRCCHLKT IWSAPLPPQT EIAREMTTGS TTIDIMGLQS AYAKLHTDQE RDYFMQRYRD VISSFGGKTS YDADNRPLLL MR SNFWASG YDVDGTDQTS LGQFSGRVQQ TFKHAVPRFF VPEHGVIMTL ALVRFPPTCT EEHHYLIGKG SLTYTDLAGD PTL VGNLPP REIAMENLFR SGGTGTDQKF KVAESIWYRY HPSYVDSAYH LLEGFPFLQG RPAGNMTERV LIDHTKYDSC FQST QLGQW NAQAKFNVSV YRSIPTVRDS IMTS

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Macromolecule #2: spike protein G

MacromoleculeName: spike protein G / type: protein_or_peptide / ID: 2 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage PJNS002 (virus)
Molecular weightTheoretical: 18.864549 KDa
SequenceString:
MFQEFVSKHN SPFTSLPMVS KSVTPSVTAA PILSTPRNQQ VTESFLDLTI ATAAGGIASI ISVDPSAKAD NQVFSVCAHL TGAADLKYW AALVRFESAT VPTTVTPTFD LFPIAGTYSN GTYIVKDCAT IKTFPNVAGN TVYVGLMLFS NSWVAGKLTG I ISINQVRT EITTLQPLK

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Macromolecule #3: DNA-binding protein J

MacromoleculeName: DNA-binding protein J / type: protein_or_peptide / ID: 3 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage PJNS002 (virus)
Molecular weightTheoretical: 2.929386 KDa
SequenceString:
MAKSYRRGSS GKKKGSRLWY VGGSQF

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Macromolecule #4: DNA (5'-D(P*AP*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*AP*A)-3') / type: dna / ID: 4 / Number of copies: 60 / Classification: DNA
Source (natural)Organism: Salmonella phage PJNS002 (virus)
Molecular weightTheoretical: 1.521077 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)

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Macromolecule #5: DNA (5'-D(P*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*A)-3') / type: dna / ID: 5 / Number of copies: 60 / Classification: DNA
Source (natural)Organism: Salmonella phage PJNS002 (virus)
Molecular weightTheoretical: 1.20787 KDa
SequenceString:
(DA)(DA)(DA)(DA)

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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
Component:
ConcentrationFormulaName
137.0 mmol/LNaClsodium chloride
2.65 mmol/LKClpotassium chloride
10.0 mmol/LNa2HPO4dibasic sodium phosphate
1.75 mmol/LKH2PO4potassium dihydrogen phosphate

Details: pH 7.2~7.6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 3827 / Average exposure time: 1.25 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 528658
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.1) / Number images used: 86486
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 18.15
Output model

PDB-9k3n:
The structure of Salmonella phage PJNS002

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