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

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Open data


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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: To Be Published
Title: Structural and Functional Insights into Microviridae PJNS001 and PJNS002 target Salmonella
Authors: Hu WL / Gao Y
History
DepositionOct 19, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 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

Projections

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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