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- EMDB-51699: Cryo-EM structure of the capsid-forming phage-inducible chromosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-51699
TitleCryo-EM structure of the capsid-forming phage-inducible chromosomal island (cf-PICI) EcCI2
Map data
Sample
  • Virus: EcCIEDL933 (bacteria)
    • Protein or peptide: Major head protein
KeywordsPICI / cf-PICI / bacteriophage / capsid / phage-inducible chromosomal island / VIRUS LIKE PARTICLE
Function / homology: / Phage capsid / Phage capsid family / Major head protein
Function and homology information
Biological speciesEscherichia coli O157:H7 str. EDL933 (bacteria) / EcCIEDL933 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsPatkowski JB / Penades JR / Costa TRD
Funding support United Kingdom, European Union, 5 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Engineering and Physical Sciences Research Council United Kingdom
European Research Council (ERC)European Union
CitationJournal: Cell / Year: 2025
Title: Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization.
Authors: Lingchen He / Jonasz B Patkowski / Jinlong Wang / Laura Miguel-Romero / Christopher H S Aylett / Alfred Fillol-Salom / Tiago R D Costa / José R Penadés /
Abstract: Some mobile genetic elements spread among unrelated bacterial species through unknown mechanisms. Recently, we discovered that identical capsid-forming phage-inducible chromosomal islands (cf-PICIs), ...Some mobile genetic elements spread among unrelated bacterial species through unknown mechanisms. Recently, we discovered that identical capsid-forming phage-inducible chromosomal islands (cf-PICIs), a new family of phage satellites, are present across multiple species and genera, raising questions about their widespread dissemination. Here, we have identified and characterized a new biological entity enabling this transfer. Unlike other satellites, cf-PICIs produce their own capsids and package their DNA, relying solely on phage tails for transfer. cf-PICIs release non-infective, tailless capsids containing their DNA into the environment. These subcellular entities then interact with phage tails from various species, forming chimeric particles that inject DNA into different bacterial species depending on the tail present. Additionally, we elucidated the structure of the tailless cf-PICIs and the mechanism behind their unique capsid formation. Our findings illuminate the mechanisms used by satellites to spread in nature, contributing to bacterial evolution and the emergence of new pathogens.
History
DepositionOct 2, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51699.png

Downloads & links

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Map

FileDownload / File: emd_51699.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 500 pix.
= 715. Å		1.43 Å/pix.
x 500 pix.
= 715. Å		1.43 Å/pix.
x 500 pix.
= 715. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-1.0565522 - 2.4741533
Average (Standard dev.)0.012635004 (±0.14362282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 715.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51699_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_51699_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : EcCIEDL933

EntireName: EcCIEDL933 (bacteria)
Components
  • Virus: EcCIEDL933 (bacteria)
    • Protein or peptide: Major head protein

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Supramolecule #1: EcCIEDL933

SupramoleculeName: EcCIEDL933 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 155864 / Sci species name: EcCIEDL933 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: EcCIEDL933 cf-PICI capsid / Diameter: 475.0 Å / T number (triangulation number): 4

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Macromolecule #1: Major head protein

MacromoleculeName: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O157:H7 str. EDL933 (bacteria) / Strain: EDL933
Molecular weightTheoretical: 43.17543 KDa
SequenceString: MPRIIELRQQ KTAIKNQMRD MLENAEKENR SLNDAEGAKF DELRAKAESL DKDISRLEAI ADEERSKPGK SSQTTDPAEL RNYILTGET RALSTGVPAD GGYTVIPELN TEIMRMLTDE STMRRICTVK KISSNEFKQL VSAGGATVNH GEEGKTREQT S TPQINEVS ...String:
MPRIIELRQQ KTAIKNQMRD MLENAEKENR SLNDAEGAKF DELRAKAESL DKDISRLEAI ADEERSKPGK SSQTTDPAEL RNYILTGET RALSTGVPAD GGYTVIPELN TEIMRMLTDE STMRRICTVK KISSNEFKQL VSAGGATVNH GEEGKTREQT S TPQINEVS IKLYPVYAYP RTTQEIVDFS DVDILSWLTG EIGDTFTETE ESDLVVGDGD KKAKGFLSVP RAEKNDKERD FG TLQVIKP SESLAWTSAD PLIDLKFALR KKYRKNAVWV VNSTTAAKLQ KVKNANGDYI WRDRLQAGDP DTLLGLPVEY LEF MPDNVI ALGDFKRGYY IVDHETGVRT RPDNLTEPGF IKIFTQKYLG GGVVDSNAIK ILELPQDDD

UniProtKB: Major head protein

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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

BufferpH: 8.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1993
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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