9RCE | pdb_00009rce

Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the baseplate 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
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wwPDB Validation 3D Report Full Report

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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: 797.63 kDa 
  • Atom Count: 50,351 
  • Modeled Residue Count: 6,322 
  • Deposited Residue Count: 7,092 
  • Unique protein chains: 9

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidoglycan-binding proteinA [auth H],
G [auth M]
217Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: GND90_001406
UniProt
Find proteins for A0A730ZGQ3 (Salmonella enterica subsp. houtenae serovar 1,40:z4,z32:-)
Explore A0A730ZGQ3 
Go to UniProtKB:  A0A730ZGQ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A730ZGQ3
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Conserved hypothetical phage tail region proteinB [auth I],
I [auth N]
158Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: NCTC10718_02962
UniProt
Find proteins for A0A379QYS5 (Salmonella enterica)
Explore A0A379QYS5 
Go to UniProtKB:  A0A379QYS5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A379QYS5
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
SalCis12C [auth B],
J
804Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: GND90_001400
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
GPW/gp25 family proteinD [auth C],
K
149Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: GND90_001403
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Phage tail sheath family proteinE [auth D],
L
519Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: G0C45_16390
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
SalCis6F [auth E]56Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: NCTC10718_02961
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Type VI secretion system tip protein VgrGH [auth F]597Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: vgrGGND90_001405
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
SalCis10M [auth c]99Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: NCTC10718_02958
UniProt
Find proteins for A0A379R0X0 (Salmonella enterica)
Explore A0A379R0X0 
Go to UniProtKB:  A0A379R0X0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A379R0X0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate protein J-like domain-containing proteinN [auth A],
O [auth G]
1,323Salmonella enterica subsp. salamaeMutation(s): 0 
Gene Names: GND90_001402

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

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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