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- PDB-9gyi: Cryo-EM structure of the capsid-forming phage-inducible chromosom... -

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Basic information

Entry
Database: PDB / ID: 9gyi
TitleCryo-EM structure of the capsid-forming phage-inducible chromosomal island (cf-PICI) EcCI2
ComponentsMajor head protein
KeywordsVIRUS LIKE PARTICLE / PICI / cf-PICI / bacteriophage / capsid / phage-inducible chromosomal island
Function / homology: / Phage capsid / Phage capsid family / Major head protein
Function and homology information
Biological speciesEscherichia coli O157:H7 str. EDL933 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsPatkowski, J.B. / Penades, J.R. / Costa, T.R.D.
Funding support United Kingdom, European Union, 5items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Sep 24, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Major head protein
C: Major head protein
D: Major head protein
A: Major head protein


Theoretical massNumber of molelcules
Total (without water)172,7024
Polymers172,7024
Non-polymers00
Water00
1
B: Major head protein
C: Major head protein
D: Major head protein
A: Major head protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,362,103240
Polymers10,362,103240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Major head protein
C: Major head protein
D: Major head protein
A: Major head protein
x 5


  • icosahedral pentamer
  • 864 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)863,50920
Polymers863,50920
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
B: Major head protein
C: Major head protein
D: Major head protein
A: Major head protein
x 6


  • icosahedral 23 hexamer
  • 1.04 MDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)1,036,21024
Polymers1,036,21024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major head protein


Mass: 43175.430 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Escherichia coli O157:H7 str. EDL933 (bacteria)
Strain: EDL933 / References: UniProt: Q8X755
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: EcCIEDL933 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: EcCIEDL933 (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Virus shellName: EcCIEDL933 cf-PICI capsid / Diameter: 475 nm / Triangulation number (T number): 4
Buffer solutionpH: 8.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1993 / Symmetry type: POINT

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