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- EMDB-54016: SPP1 Procapid I in cellula -

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Basic information

Entry
Database: EMDB / ID: EMD-54016
TitleSPP1 Procapid I in cellula
Map dataProcapsid I map from SVA on lamella
Sample
  • Virus: Bacillus phage SPP1 (virus)
KeywordsSPP1 Procapsid I SVA / VIRUS
Biological speciesBacillus phage SPP1 (virus)
Methodelectron tomography / cryo EM
AuthorsCorroyer-Dulmont S / Labarde A / Prazak V / Godinho L / Masson C / Legrand P / Gruenewald K / Tavares P / Quemin ERJ
Funding support France, Germany, 3 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE12-0019-01 France
ATIP-Avenir France
German Research Foundation (DFG)INST 152/772-1, 774-1, 775-1, 777-1 Germany
CitationJournal: To Be Published
Title: SPP1_Procapsid_I_in_cellula
Authors: Corroyer-Dulmont S / Labarde A / Prazak V / Godinho L / Masson C / Legrand P / Gruenewald K / Tavares P / Quemin ERJ
History
DepositionJun 14, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54016.png

Downloads & links

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Map

FileDownload / File: emd_54016.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProcapsid I map from SVA on lamella
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.6 Å/pix.
x 80 pix.
= 688. Å		8.6 Å/pix.
x 80 pix.
= 688. Å		8.6 Å/pix.
x 80 pix.
= 688. Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.6 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-9.155170999999999 - 7.033722
Average (Standard dev.)-2.31497 (±1.6714419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 688.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Bacillus phage SPP1

EntireName: Bacillus phage SPP1 (virus)
Components
  • Virus: Bacillus phage SPP1 (virus)

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Supramolecule #1: Bacillus phage SPP1

SupramoleculeName: Bacillus phage SPP1 / type: virus / ID: 1 / Parent: 0
Details: SPP1 bacterial virus multiplied by infection of Bacillus subtilis strain YB886
NCBI-ID: 10724 / Sci species name: Bacillus phage SPP1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Virus shellShell ID: 1 / Name: Major Capsid Protein gp13 / Diameter: 550.0 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 180.0 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: 2.6 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 40
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION

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