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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: 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_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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