9R9N | pdb_00009r9n

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9R9N

This is version 1.1 of the entry. See complete history

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 

  • 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.


  • Organizational Affiliation
    • Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Macromolecule Content 

  • Total Structure Weight: 125.93 kDa 
  • Atom Count: 8,640 
  • Modeled Residue Count: 1,102 
  • Deposited Residue Count: 1,129 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phage tail sheath family protein519Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: G0C45_16390
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF4255 domain-containing protein194Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: G0C45_16400
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Phage tail proteinC [auth D]156Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: G0C45_16385
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SalCis16b - capD [auth C]260Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: GND90_001410

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC4.6.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Independent Research Fund Denmark - Medical SciencesDenmark30342400-1201051001

Revision History  (Full details and data files)

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