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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: Nat Commun / Year: 2026
Title: Subcellular reorganization upon phage infection reveals stepwise assembly of viral particles from membrane-associated precursors.
Authors: Simon Corroyer-Dulmont / Audrey Labarde / Vojtěch Pražák / Lia M Godinho / Chloé Masson / Pierre Legrand / Kay Grünewald / Paulo Tavares / Emmanuelle R J Quemin /
Abstract: Viruses are obligate intracellular parasites and viral infections lead to massive host cell rearrangement to support the rapid generation of progeny. Host take-over and remodelling include formation ...Viruses are obligate intracellular parasites and viral infections lead to massive host cell rearrangement to support the rapid generation of progeny. Host take-over and remodelling include formation of viral-induced compartments for viral genome replication and/or assembly. While viruses infecting bacteria, bacteriophages or phages, have been extensively characterized in vitro, the molecular mechanisms underlying the viral cycle inside the crowded cytoplasm remain unclear. Here, we investigate the spatial reorganization of SPP1-infected bacteria under near-native conditions by electron cryo tomography. The most prominent feature is the formation of a large viral DNA (vDNA) compartment from which ribosomes are excluded. In SPP1 infection, there is no membrane nor proteinaceous shell surrounding these compartments. Also, we identify novel key intermediates in virus assembly: open precursors of procapsid lattice are found at the cytoplasmic membrane in a process that requires expression of the portal protein. Next, DNA-free procapsids relocate inside the vDNA compartment where vDNA is packed in a stepwise manner. Finally, DNA-filled capsids segregate to the periphery of the compartment for assembly completion and storage. Collectively, we provide comprehensive mechanistic insights into the complete viral assembly pathway of SPP1 directly in cellula and show how specific steps are coordinated inside the reorganized bacterial cell.
History
DepositionJun 14, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 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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