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- EMDB-62020: The Map of PJNS002 spike protein G with Salmonella enterica LPS -

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Basic information

Entry
Database: EMDB / ID: EMD-62020
TitleThe Map of PJNS002 spike protein G with Salmonella enterica LPS
Map data
Sample
  • Complex: PJNS002 spike protein G incubated with LPS
KeywordsLPS / VIRAL PROTEIN
Biological speciesMicroviridae (isometric ssDNA phages)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 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_62020.png

Downloads & links

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Map

FileDownload / File: emd_62020.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 160 pix.
= 131.2 Å		0.82 Å/pix.
x 160 pix.
= 131.2 Å		0.82 Å/pix.
x 160 pix.
= 131.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.16641128 - 0.3355921
Average (Standard dev.)0.0027272308 (±0.012659119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 131.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62020_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_62020_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PJNS002 spike protein G incubated with LPS

EntireName: PJNS002 spike protein G incubated with LPS
Components
  • Complex: PJNS002 spike protein G incubated with LPS

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Supramolecule #1: PJNS002 spike protein G incubated with LPS

SupramoleculeName: PJNS002 spike protein G incubated with LPS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Microviridae (isometric ssDNA phages) / Strain: PJNS002
Molecular weightTheoretical: 100 KDa

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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

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mmol/LNaClsodium chloride
20.0 mmol/L2-Amino-2-(hydroxymethyl)-1,3-propanediolTris base
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 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: 3515 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Details: A total of 712, 1,940 and 863 frame stacks were collected at tilt angles of 0, 15 and 30 degree, respectively.
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: 29000
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: 1755511
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: use EMAN2 to convert the model containing pentameric G to density map
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 238773
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.1)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: EMAN2
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 18.15

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