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- EMDB-53859: Cryo-EM structure of a contractile injection system in Salmonella... -

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Basic information

Entry
Database: EMDB / ID: EMD-53859
TitleCryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
Map dataSalCIS Cap C6 reconstruction
Sample
  • Complex: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: DUF4255 domain-containing protein
    • Protein or peptide: SalCis16b - cap
    • Protein or peptide: Phage tail protein
Keywordscontractile injection system Salmonella / CONTRACTILE PROTEIN
Biological speciesSalmonella enterica subsp. salamae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsEjaz RN / Tillmann HP / Sofos NH / Siborova M / Taylor NMI
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_53859.png

Downloads & links

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Map

FileDownload / File: emd_53859.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSalCIS Cap C6 reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 261. Å		0.73 Å/pix.
x 360 pix.
= 261. Å		0.73 Å/pix.
x 360 pix.
= 261. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0493
Minimum - Maximum-0.26410335 - 0.4312338
Average (Standard dev.)0.0048509105 (±0.030197876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SalCIS Cap C6 reconstruction half map A

Fileemd_53859_half_map_1.map
AnnotationSalCIS Cap C6 reconstruction half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SalCIS Cap C6 reconstruction half map B

Fileemd_53859_half_map_2.map
AnnotationSalCIS Cap C6 reconstruction 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 : Cryo-EM structure of a contractile injection system in Salmonella...

EntireName: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
Components
  • Complex: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: DUF4255 domain-containing protein
    • Protein or peptide: SalCis16b - cap
    • Protein or peptide: Phage tail protein

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Supramolecule #1: Cryo-EM structure of a contractile injection system in Salmonella...

SupramoleculeName: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4, #3
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: 1 / 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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Macromolecule #2: DUF4255 domain-containing protein

MacromoleculeName: DUF4255 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 22.038859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLDLCLNYLK ERMNQSVKNV FDLADDLVIV SPPTDLDGSK LPKIQNKILI FISNIEKDSF SKSYRQDFNH TSNRTAVSSQ PLFITITVT VAANFSTNHY SDGLKVLSHF LAFFNRHNSF NRQNSPDLPK NIEQLNMELD SIPGDQLNHL WGIFGSHYLP S CTYRVRAL ...String:
MLDLCLNYLK ERMNQSVKNV FDLADDLVIV SPPTDLDGSK LPKIQNKILI FISNIEKDSF SKSYRQDFNH TSNRTAVSSQ PLFITITVT VAANFSTNHY SDGLKVLSHF LAFFNRHNSF NRQNSPDLPK NIEQLNMELD SIPGDQLNHL WGIFGSHYLP S CTYRVRAL IPDSESILTQ VGNIHLSDTT LAKRDN

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Macromolecule #3: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 17.091271 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADDGSAQSD TVWPMPKFYF EVKWDGGAGA EMVSAFQEVS GLDSEAQPIE YRAGNSPVFS TIKMPGLIKS GNVTLKKGTF KGDNKFYEW YSKIKMNTIA RTAVTINLLD ESGAPVMSWK LKNAWPTKVT GTDLKSDSNE VAVETIELAH EGLEISV

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Macromolecule #4: SalCis16b - cap

MacromoleculeName: SalCis16b - cap / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 29.448793 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADYQTILTI SVLHEYYNAS SDKFAPIGLV ADRETVLLLR QYGILLKSAR GFTRLIVDTV RYSDLADLTA ELTFRFYLVS TDPGFRNIT KMPDMFDISI LNAEFTDSSE LNITAEHWVD VNQLNTSTAI DSAVIHNKNF IGLLTISLPK SHCTLEKKNI T VRFNAISA ...String:
MADYQTILTI SVLHEYYNAS SDKFAPIGLV ADRETVLLLR QYGILLKSAR GFTRLIVDTV RYSDLADLTA ELTFRFYLVS TDPGFRNIT KMPDMFDISI LNAEFTDSSE LNITAEHWVD VNQLNTSTAI DSAVIHNKNF IGLLTISLPK SHCTLEKKNI T VRFNAISA YWKYYIFSPG GKKNLNIPHS FTEQEPEQVA NKTARIFMSD NPILLRKIYA EPFSLLDANN VIIKSLPLPM PD NISTSIV KGFKITIAHI YIN

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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: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER / Details: 5mA
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 18 / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 5471
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 20

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9r9n:
Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.

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