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- EMDB-74608: Cryo-ET of non-symmetric viruses from partially irrigated soils v... -

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Basic information

Entry
Database: EMDB / ID: EMD-74608
TitleCryo-ET of non-symmetric viruses from partially irrigated soils volume 1
Map data3d tomogram reconstructed at a final binning of 8x relative to the raw tilt series.No subvolume averaging, contains several virus like particles (vlps)
SampleSoil bacteriophage/vlp obtained from partially irrigated soils != unidentified

Soil bacteriophage/vlp obtained from partially irrigated soils

  • Virus: unidentified (others)
Keywordssoil bacteriophage / virus like particle / VIRUS
Biological speciesunidentified (others)
Methodelectron tomography / cryo EM / Resolution: 8.9 Å
AuthorsParvate AD / Alfaro T / McDearis R / Zimmerman A / Hofmockel KC / Nelson WC / Evans JE
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)79415 United States
Department of Energy (DOE, United States)D7G33 United States
CitationJournal: Front Agron / Year: 2026
Title: Cryo-EM visualization of viruses from partially irrigated soils
Authors: Parvate AD / Alfaro T / McDearis R / Zimmerman AE / Hofmockel KS / Nelson WC / Evans JE
History
DepositionDec 19, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74608.png

Downloads & links

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Map

FileDownload / File: emd_74608.map.gz / Format: CCP4 / Size: 367 MB / Type: IMAGE STORED AS SIGNED BYTE
Annotation3d tomogram reconstructed at a final binning of 8x relative to the raw tilt series.No subvolume averaging, contains several virus like particles (vlps)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.9 Å/pix.
x 261 pix.
= 2322.9 Å		8.9 Å/pix.
x 1440 pix.
= 12815.999 Å		8.9 Å/pix.
x 1024 pix.
= 9113.6 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.9 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)47.636012999999998 (±7.6892967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-9493-82
Dimensions14401024261
Spacing10241440261
CellA: 9113.6 Å / B: 12815.999 Å / C: 2322.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Soil bacteriophage/vlp obtained from partially irrigated soils

EntireName: Soil bacteriophage/vlp obtained from partially irrigated soils
Components
  • Virus: unidentified (others)

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Supramolecule #1: unidentified

SupramoleculeName: unidentified / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 32644 / Sci species name: unidentified / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: unidentified (others)
Virus shellShell ID: 1 / Name: Unknown

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
Details: PPBS: 2% bovine serum albumin, 10% phosphate-buffered saline, 1% potassium citrate, and 150 mM MgSO4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP
DetailsEnvironmental sample containing mixuture of naturally occuring bacteriophages
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 41 / Average exposure time: 0.32 sec. / Average electron dose: 1.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 41000
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 reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: OTHER / Software - Name: eTomo
Details: 8.9 angstrom is the final pixel size of the binned 3d volume.
Number images used: 41
CTF correctionSoftware - Name: eTomo
Details: CTF correction carried out during the Etomo reconstruction workflow
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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