[English] 日本語
Yorodumi
- PDB-9rce: Cryo-EM structure of a contractile injection system in Salmonella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rce
TitleCryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the baseplate portion in extended state.
Components
  • Baseplate protein J-like domain-containing protein
  • Conserved hypothetical phage tail region protein
  • GPW/gp25 family protein
  • Peptidoglycan-binding protein
  • Phage tail sheath family protein
  • SalCis10
  • SalCis12
  • SalCis6
  • Type VI secretion system tip protein VgrG
KeywordsCONTRACTILE PROTEIN / contractile injection system Salmonella
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / PAAR motif / PAAR motif / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / LysM domain profile. / LysM domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Conserved hypothetical phage tail region protein / Uncharacterized conserved protein / Peptidoglycan-binding protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. salamae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsEjaz, R.N. / Tillmann, H.P. / Sofos, N.H. / Siborova, M. / Taylor, N.M.I.
Funding support Denmark, 1items
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 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.1May 6, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Peptidoglycan-binding protein
I: Conserved hypothetical phage tail region protein
B: SalCis12
C: GPW/gp25 family protein
D: Phage tail sheath family protein
E: SalCis6
M: Peptidoglycan-binding protein
F: Type VI secretion system tip protein VgrG
N: Conserved hypothetical phage tail region protein
J: SalCis12
K: GPW/gp25 family protein
L: Phage tail sheath family protein
c: SalCis10
A: Baseplate protein J-like domain-containing protein
G: Baseplate protein J-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)797,62715
Polymers797,62715
Non-polymers00
Water00
1
H: Peptidoglycan-binding protein
I: Conserved hypothetical phage tail region protein
B: SalCis12
C: GPW/gp25 family protein
D: Phage tail sheath family protein
E: SalCis6
M: Peptidoglycan-binding protein
F: Type VI secretion system tip protein VgrG
N: Conserved hypothetical phage tail region protein
J: SalCis12
K: GPW/gp25 family protein
L: Phage tail sheath family protein
A: Baseplate protein J-like domain-containing protein
G: Baseplate protein J-like domain-containing protein

H: Peptidoglycan-binding protein
I: Conserved hypothetical phage tail region protein
B: SalCis12
C: GPW/gp25 family protein
D: Phage tail sheath family protein
E: SalCis6
M: Peptidoglycan-binding protein
F: Type VI secretion system tip protein VgrG
N: Conserved hypothetical phage tail region protein
J: SalCis12
K: GPW/gp25 family protein
L: Phage tail sheath family protein
A: Baseplate protein J-like domain-containing protein
G: Baseplate protein J-like domain-containing protein

H: Peptidoglycan-binding protein
I: Conserved hypothetical phage tail region protein
B: SalCis12
C: GPW/gp25 family protein
D: Phage tail sheath family protein
E: SalCis6
M: Peptidoglycan-binding protein
F: Type VI secretion system tip protein VgrG
N: Conserved hypothetical phage tail region protein
J: SalCis12
K: GPW/gp25 family protein
L: Phage tail sheath family protein
A: Baseplate protein J-like domain-containing protein
G: Baseplate protein J-like domain-containing protein

c: SalCis10


Theoretical massNumber of molelcules
Total (without water)2,373,73443
Polymers2,373,73443
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation2

-
Components

-
Protein , 9 types, 15 molecules HMINBJCKDLEFcAG

#1: Protein Peptidoglycan-binding protein


Mass: 23868.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: GND90_001406 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A730ZGQ3
#2: Protein Conserved hypothetical phage tail region protein


Mass: 17506.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: NCTC10718_02962 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A379QYS5
#3: Protein SalCis12


Mass: 93034.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: GND90_001400 / Production host: Escherichia coli (E. coli)
#4: Protein GPW/gp25 family protein


Mass: 16921.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: GND90_001403 / Production host: Escherichia coli (E. coli)
#5: Protein Phage tail sheath family protein


Mass: 57351.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: G0C45_16390 / Production host: Escherichia coli (E. coli)
#6: Protein SalCis6


Mass: 6294.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: NCTC10718_02961 / Production host: Escherichia coli (E. coli)
#7: Protein Type VI secretion system tip protein VgrG


Mass: 63170.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: vgrG, GND90_001405 / Production host: Escherichia coli (E. coli)
#8: Protein SalCis10


Mass: 9573.319 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: NCTC10718_02958 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A379R0X0
#9: Protein Baseplate protein J-like domain-containing protein


Mass: 150611.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. salamae (bacteria)
Gene: GND90_001402 / Production host: Escherichia coli (E. coli)

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Cryo-EM structure of a contractile injection system in Salmonella enterica subspecies Salamae, the cap portion in extended state.
Type: COMPLEX / Entity ID: #1-#2, #9, #3 / Source: RECOMBINANT
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2PHENIX1.21_5207model refinement
5cryoSPARC4.6.0CTF correction
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20065 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 108.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002951525
ELECTRON MICROSCOPYf_angle_d0.55469943
ELECTRON MICROSCOPYf_chiral_restr0.04357835
ELECTRON MICROSCOPYf_plane_restr0.00439013
ELECTRON MICROSCOPYf_dihedral_angle_d15.361618814

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more