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- EMDB-53858: Cryo-EM structure of an extracellular contractile injection syste... -

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Basic information

Entry
Database: EMDB / ID: EMD-53858
TitleCryo-EM structure of an extracellular contractile injection system in Salmonella enterica subspecies salamae, the sheath in contracted state.
Map dataSalCIS contracted sheath helical refinement
Sample
  • Complex: Helical assembly of a contractile injection system, in contracted form
    • Protein or peptide: Phage tail sheath family protein
KeywordsContractile injections system / Salmonella enterica subspecies salamae / CONTRACTILE PROTEIN
Biological speciesSalmonella enterica subsp. salamae (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsEjaz RN / Tillmann HP / Taylor NMI / Siborova M / Sofos NH
Funding support Denmark, 1 items
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, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53858.png

Downloads & links

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Map

FileDownload / File: emd_53858.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSalCIS contracted sheath helical refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 400 pix.
= 640. Å		1.6 Å/pix.
x 400 pix.
= 640. Å		1.6 Å/pix.
x 400 pix.
= 640. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.519
Minimum - Maximum-2.2637343 - 5.372701
Average (Standard dev.)0.0051973364 (±0.28983513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 640.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SalCIS contracted sheath helical refinement half map A

Fileemd_53858_half_map_1.map
AnnotationSalCIS contracted sheath helical refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SalCIS contracted sheath helical refinement half map B

Fileemd_53858_half_map_2.map
AnnotationSalCIS contracted sheath helical refinement half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical assembly of a contractile injection system, in contracted form

EntireName: Helical assembly of a contractile injection system, in contracted form
Components
  • Complex: Helical assembly of a contractile injection system, in contracted form
    • Protein or peptide: Phage tail sheath family protein

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Supramolecule #1: Helical assembly of a contractile injection system, in contracted form

SupramoleculeName: Helical assembly of a contractile injection system, in contracted form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)

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Macromolecule #1: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 57.35193 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGVMKTPGVY IVEQNAFPNS VVEVATAVPA FIGYTEKADN GGKSLSNKGW RITSMSEYRQ YFGGEPQHLF EISEISTTSN ANIREAFKQ SGKTYQITQS NTRHHLYYSM LFFFQNGGGP CYIVSVGNYS DDIDAAVLKG GILPLIKEAE PTMLLIPEAI Q LAEDDCIN ...String:
MGVMKTPGVY IVEQNAFPNS VVEVATAVPA FIGYTEKADN GGKSLSNKGW RITSMSEYRQ YFGGEPQHLF EISEISTTSN ANIREAFKQ SGKTYQITQS NTRHHLYYSM LFFFQNGGGP CYIVSVGNYS DDIDAAVLKG GILPLIKEAE PTMLLIPEAI Q LAEDDCIN VEQAMLGHCG GKMKNRVAIL DVWNGYKDRQ HPDGDCVESF RSKLGTHYLD YAAAYYPWLN TSIVQDSDVS FL NISNIDK LAELLSGEVA LMFSDLEGLS EEELSTGGNK LRATRKQAML DEIAKLSAEI SRPDAVLLHK ILSNMSPLYQ TIM ADIKFQ QNILPPSSAM AGIYTMVDNS RGVWKAPANV SVNAVVSPTV NISDDEQEDL NVTTQGKSIN AIRPFIGEGT LVWG ARTLD GNSVDWRYIN VRRTMIMLEE SIKLASKAYV FEPNVANTWV SMESMLSNFL YGIWKRGGLA GSTPGEAYNV SVGLG KTMT SNDILEGILR ITVLVAMVRP AEFIEITFQQ KMQES

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

Concentration15 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsHeterogenous sample of purified contractile injection system

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 8060 / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 17.742 Å
Applied symmetry - Helical parameters - Δ&Phi: 28 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227055
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 3479786
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9r9i:
Cryo-EM structure of an extracellular contractile injection system in Salmonella enterica subspecies salamae, the sheath in contracted state.

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