9R9H | pdb_00009r9h

Cryo-EM structure of an extracellular contractile injection system in Salmonella enterica subspecies salamae, the sheath and inner tube module in extended state.

• PDB DOI: https://doi.org/10.2210/pdb9R9H/pdb
• EM Map EMD-53857: EMDB EMDataResource

• Classification: CONTRACTILE PROTEIN
• Organism(s): Salmonella enterica subsp. salamae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-20 Released: 2026-04-22 
• Deposition Author(s): Ejaz, R.N., Tillmann, H.P., Sofos, N.H., Siborova, M., Taylor, N.M.I.
• Funding Organization(s): Independent Research Fund Denmark - Medical Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.28 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Structure of a contractile injection system in Salmonella enterica subsp. salamae.

Ejaz, R.N., Funke, K., Kielkopf, C.S., Martin, F.J.O., Siborova, M., Hendriks, I.A., Sofos, N.H., Pape, T., Steiner-Rebrova, E.M., Nielsen, M.L., Erhardt, M., Taylor, N.M.I.

(2026) Nat Commun 

• PubMed: 41991534 
• DOI: https://doi.org/10.1038/s41467-026-71989-6
• Primary Citation Related Structures: 
  9R9A, 9R9H, 9R9I, 9R9N, 9RCE


• PubMed 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 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.

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Organizational Affiliation: 
• Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Novo Nordisk Foundation Centre for Protein Research, ICMM, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Institute of Biology-Department of Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany.
Core Facility for Integrated Bioimaging, Centre for Core Facilities (CCF), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Biomedical Centre, Department of Experimental Medical Science, Faculty of Medicine, University of Lund, Lund, Sweden.
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
Institute of Biology-Department of Molecular Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Max Planck Unit for the Science of Pathogens, Berlin, Germany.
Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [e-mail].
Novo Nordisk Foundation Centre for Protein Research, ICMM, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 36-mer - A18B18 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,339.98 kDa 
• Atom Count: 93,006 
• Modeled Residue Count: 12,006 
• Deposited Residue Count: 12,150 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage tail sheath family protein	A [auth T], B [auth U], C [auth V], D [auth W], E [auth X], F [auth Y], G [auth Z], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f], N [auth g], O [auth h], P [auth i], Q [auth j], R [auth k]	519	Salmonella enterica subsp. salamae	Mutation(s): 0  Gene Names: G0C45_16390

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage tail protein	AA [auth J], BA [auth K], CA [auth L], DA [auth M], EA [auth N], FA [auth O], GA [auth P], HA [auth Q], IA [auth R], JA [auth S], S [auth B], T [auth C], U [auth D], V [auth E], W [auth F], X [auth G], Y [auth H], Z [auth I]	156	Salmonella enterica subsp. salamae	Mutation(s): 0  Gene Names: G0C45_16385

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.28 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC	4

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Ejaz, R.N., Tillmann, H.P., Sofos, N.H., Siborova, M., Taylor, N.M.I.

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Funding Organization	Location	Grant Number
Independent Research Fund Denmark - Medical Sciences	Denmark	30342400-1201051001

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release
  
• Version 1.1: 2026-05-06
  Changes: Data collection, Database references