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- EMDB-62021: The STA map of PJNS001 attached on Salmonella outer membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-62021
TitleThe STA map of PJNS001 attached on Salmonella outer membrane
Map data
Sample
  • Virus: Microviridae (isometric ssDNA phages)
KeywordsPJNS001 / in situ / VIRUS
Biological speciesMicroviridae (isometric ssDNA phages)
Methodsubtomogram averaging / cryo EM / Resolution: 32.3 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_62021.png

Downloads & links

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Map

FileDownload / File: emd_62021.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.72 Å/pix.
x 120 pix.
= 806.4 Å		6.72 Å/pix.
x 120 pix.
= 806.4 Å		6.72 Å/pix.
x 120 pix.
= 806.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.030662822 - 0.0615785
Average (Standard dev.)-0.00038999767 (±0.005923125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 806.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62021_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62021_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Microviridae

EntireName: Microviridae (isometric ssDNA phages)
Components
  • Virus: Microviridae (isometric ssDNA phages)

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Supramolecule #1: Microviridae

SupramoleculeName: Microviridae / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: T=1 icosahedral virus applied with C5 symmetry / NCBI-ID: 10841 / Sci species name: Microviridae / Sci species strain: PJNS001 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
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: PBS buffer
GridModel: Quantifoil R2/1 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: before plunge freezing, incubated with Salmonella under 36 degree celsius for 10 minutes.

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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 / Average exposure time: 0.45 sec. / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 6.0 µm / Calibrated defocus min: 2.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 14000
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

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 32.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number subtomograms used: 106
ExtractionNumber tomograms: 13 / Number images used: 172 / Method: manual
Software: (Name: Dynamo (ver. 1.1.532), RELION (ver. 4.0.0))
CTF correctionSoftware - Name: IMOD (ver. 4.11.24) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 4.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: PJNS001 in vivo
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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