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- PDB-9r9n: Cryo-EM structure of a contractile injection system in Salmonella... -

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Basic information

Entry
Database: PDB / ID: 9r9n
TitleCryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
Components
  • DUF4255 domain-containing protein
  • Phage tail protein
  • Phage tail sheath family protein
  • SalCis16b - cap
KeywordsCONTRACTILE PROTEIN / contractile injection system Salmonella
Biological speciesSalmonella enterica subsp. salamae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsEjaz, R.N. / Tillmann, H.P. / Sofos, N.H. / Siborova, M. / Taylor, N.M.I.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Independent Research Fund Denmark - Medical Sciences30342400-1201051001 Denmark
CitationJournal: Nat Commun / Year: 2026
Title: Structure of a contractile injection system in Salmonella enterica subsp. salamae.
Authors: Rooshanie N Ejaz / Kristin Funke / Claudia S Kielkopf / Freddie J O Martin / Marta Šiborová / Ivo A Hendriks / Nicholas H Sofos / Tillmann Pape / Eva M Steiner-Rebrova / Michael L Nielsen ...Authors: Rooshanie N Ejaz / Kristin Funke / Claudia S Kielkopf / Freddie J O Martin / Marta Šiborová / Ivo A Hendriks / Nicholas H Sofos / Tillmann Pape / Eva M Steiner-Rebrova / Michael L Nielsen / Marc Erhardt / Nicholas M I Taylor /
Abstract: Extracellular contractile injection systems (eCISs) are phage-derived nanomachines used by bacteria to deliver effectors into target cells. Well-studied examples include the Photorhabdus asymbiotica ...Extracellular contractile injection systems (eCISs) are phage-derived nanomachines used by bacteria to deliver effectors into target cells. Well-studied examples include the Photorhabdus asymbiotica virulence cassettes and the antifeeding prophage from Serratia entomophila, which have been engineered for heterologous cargo delivery. Recent genomic analyses identified eCIS gene clusters in the opportunistic human pathogen Salmonella enterica subspecies salamae, but their structure, function, and biotechnological potential remain unexplored. Here, we report a high-resolution cryo-electron microscopy structure of the S. enterica eCIS. Our atomic models reveal a distinctive sheath architecture, an expansive cage-like shell around a central spike, and an associated integral membrane protein. We identify a putative effector encoded within the operon exhibiting mild periplasmic toxicity and provide evidence that the S. enterica eCIS deviates from canonical eCISs by interacting with the inner membrane. Guided by these structural features, we uncover, to the best of our knowledge, a previously unannotated cluster of contractile injection systems (CISs). Together, our findings expand the known diversity of CISs' structures and functions, and lay the groundwork for engineering customisable protein delivery platforms.
History
DepositionMay 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage tail sheath family protein
B: DUF4255 domain-containing protein
D: Phage tail protein
C: SalCis16b - cap


Theoretical massNumber of molelcules
Total (without water)125,9314
Polymers125,9314
Non-polymers00
Water00
1
A: Phage tail sheath family protein
B: DUF4255 domain-containing protein
D: Phage tail protein
C: SalCis16b - cap
x 6


Theoretical massNumber of molelcules
Total (without water)755,58524
Polymers755,58524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein Phage tail sheath family protein


Mass: 57351.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: G0C45_16390 / Production host: Escherichia coli (E. coli)
#2: Protein DUF4255 domain-containing protein


Mass: 22038.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: G0C45_16400 / Production host: Escherichia coli (E. coli)
#3: Protein Phage tail protein


Mass: 17091.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: G0C45_16385 / Production host: Escherichia coli (E. coli)
#4: Protein SalCis16b - cap


Mass: 29448.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: GND90_001410 / Production host: Escherichia coli (E. coli)
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: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
Type: COMPLEX / Entity ID: #1-#2, #4, #3 / Source: RECOMBINANT
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 5mA / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2PHENIX1.21_5207model refinement
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5471 / Num. of class averages: 18 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 105.22 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00268821
ELECTRON MICROSCOPYf_angle_d0.512111974
ELECTRON MICROSCOPYf_chiral_restr0.0441368
ELECTRON MICROSCOPYf_plane_restr0.00371533
ELECTRON MICROSCOPYf_dihedral_angle_d13.52893228

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