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- EMDB-53855: CryoEM structure of a membrane protein associated with a contract... -

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Basic information

Entry
Database: EMDB / ID: EMD-53855
TitleCryoEM structure of a membrane protein associated with a contractile injection in Salmonella enterica subspecies salamae
Map data
Sample
  • Complex: Dimeric complex of a putitaive transmembrane hydrolase in LMNG
    • Protein or peptide: Uncharacterized protein
KeywordsHydrolase / transmembrane / contractile injection system / MEMBRANE PROTEIN
Biological speciesSalmonella enterica subsp. salamae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsEjaz RN / Tillmann HP / Taylor NMI / Siborova M / Sofos NH
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 19, 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_53855.png

Downloads & links

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Map

FileDownload / File: emd_53855.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 320 pix.
= 232.96 Å		0.73 Å/pix.
x 320 pix.
= 232.96 Å		0.73 Å/pix.
x 320 pix.
= 232.96 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.728 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03033
Minimum - Maximum-0.17410143 - 0.33150026
Average (Standard dev.)-0.00018897584 (±0.010112518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 232.95999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53855_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_53855_half_map_2.map
Projections & Slices
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Sample components

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Entire : Dimeric complex of a putitaive transmembrane hydrolase in LMNG

EntireName: Dimeric complex of a putitaive transmembrane hydrolase in LMNG
Components
  • Complex: Dimeric complex of a putitaive transmembrane hydrolase in LMNG
    • Protein or peptide: Uncharacterized protein

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Supramolecule #1: Dimeric complex of a putitaive transmembrane hydrolase in LMNG

SupramoleculeName: Dimeric complex of a putitaive transmembrane hydrolase in LMNG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Structure of a putative transmembrane hydrolase determined at 2.7 angstrom resolution. Two identical subunits form a symmetric dimer, each with three transmembrane helices embedded within a ...Details: Structure of a putative transmembrane hydrolase determined at 2.7 angstrom resolution. Two identical subunits form a symmetric dimer, each with three transmembrane helices embedded within a detergent micelle composed of LMNG. The structure provides a framework for understanding the architecture and potential mechanism of this class of integral membrane hydrolases
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)

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Macromolecule #1: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. salamae (bacteria)
Molecular weightTheoretical: 97.030258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MINPGFSLLS LISQPASRLI RRVICGLLCG GLLCTLPAIG YAAQNGLVES AQPYKTCSKQ LTATDKRNLG KAIQTQLADF YQNSSDFQA QLKRGQRLND GIVGPTTRYW LDYFCGEFAF TVPESSNDQH QVFVESLMIA LNRAAERNAL YPTWRTAITP P QLLNLTPT ...String:
MINPGFSLLS LISQPASRLI RRVICGLLCG GLLCTLPAIG YAAQNGLVES AQPYKTCSKQ LTATDKRNLG KAIQTQLADF YQNSSDFQA QLKRGQRLND GIVGPTTRYW LDYFCGEFAF TVPESSNDQH QVFVESLMIA LNRAAERNAL YPTWRTAITP P QLLNLTPT EIEIKLGLRS AGSGKNADTP KSAEPSVPEK PDSDTAPYYY QLTEKDFASL AQRQTILATF AKLEKQQFDQ RS QLYNQLS ELFAQLNIAA TPGPNINNLI KSSSIEIPHP SKSTTTSTST SINTTPPASS EGVENTSENQ SIGDTTTSPP VPS TQVINT STQSDTQMTA PQLVWQLDPD ALNKTIKQFK ITVLPEEDLK ALTPLQSEVF PSLYLFKMAI NESGVIPDSL QSYG IFKLA RKNGLSPIHA DPVRWIAPPD CGCQDSVKSI FTMGTFYGFY PYWQHLEEGQ SIDFSRLDRI GYVGAVMKPE GNGNT LVLP QNWSAEKEFS QFIQTTHRYR TKLDLVVTTP RDLSRDQLTG LFTDDMVKQL IEAATMPMDK YVINNLKPWI SFGLQG VPS MADGITLDID LTVLDTPESQ QAFFSFLDRL KIALRQSDFR QSSAEELNGP LTSDDKYFLS VIVPVSDVVE RGNRFYN FH NFNALSKRTN LLIMRPGSPA TREKAADELD QIKGLQRWLS KQPDQLDVQQ VYKHLVPMLI SEDNRDQTTA LTQLVNLS S WSFLGAGYWP LPLSDTNEKL IDKTFFPEAQ QYPQPINQVL NSVTRLLNWI CIHRWELRTG LFVSFFFILL FLIICIWSY PLRKHLSRFP FVALTALSIS GLMLVFVADP AFQAYQGPIL IIFMIMIGWI LFAVRMVRKE GDKP

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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

Concentration3.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsA monodisperse sample of purified protein

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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) / Number grids imaged: 1 / Number real images: 42067 / 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

Particle selectionNumber selected: 12192110
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 239630
Initial angle assignmentType: OTHER
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 8

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9r9a:
CryoEM structure of a membrane protein associated with a contractile injection in Salmonella enterica subspecies salamae

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