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- EMDB-66214: CryoEM structure of the proximal sheath layer connected to the ba... -

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Basic information

Entry
Database: EMDB / ID: EMD-66214
TitleCryoEM structure of the proximal sheath layer connected to the baseplate wedge in the contracted AlgoCIS
Map data
Sample
  • Complex: Contractile injection system in marine bacterium Algoriphagus machipongonensis
KeywordsContractile injection system / CryoEM / marine bacterium / STRUCTURAL PROTEIN
Biological speciesAlgoriphagus machipongonensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXu J / Ericson CF / Toenshoff ER / Pilhofer M
Funding support Switzerland, European Union, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179255 Switzerland
Swiss National Science Foundation310030_212592 Switzerland
European Research Council (ERC)679209European Union
European Research Council (ERC)101000232European Union
CitationJournal: Nat Commun / Year: 2026
Title: Stepwise firing mechanism of an extracellular contractile injection system.
Authors: Jingwei Xu / Charles F Ericson / Elena R Toenshoff / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) mediate cell-cell interactions and are widespread among bacteria and archaea. These phage tail-like macromolecular machines puncture their target by a tube that ...Contractile injection systems (CISs) mediate cell-cell interactions and are widespread among bacteria and archaea. These phage tail-like macromolecular machines puncture their target by a tube that is propelled by a contractile sheath. The mechanism underlying CIS firing, which starts with target binding and ends with sheath contraction, remains unclear. Here, we investigate the extracellular CIS from Algoriphagus machipongonensis (AlgoCIS) by a multimodal cryo-electron microscopy approach and structure-guided engineering, which allowed us to arrest AlgoCIS in multiple intermediate states of firing. Together with the post-firing structure, our data suggest a stepwise firing mechanism involving all structural modules: signal propagation starts with the binding of the tail-fibers, followed by opening of the cage, an expansion of the baseplate iris, and resulting in sheath contraction and the release of cap adaptor. Our study will serve as a framework for understanding the firing mechanism of diverse CISs and will facilitate the engineering of CISs for biomedical applications.
History
DepositionSep 15, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_66214.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 560 pix.
= 616. Å
1.1 Å/pix.
x 560 pix.
= 616. Å
1.1 Å/pix.
x 560 pix.
= 616. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.09431864 - 0.15371174
Average (Standard dev.)0.0003087022 (±0.0041556046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 616.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66214_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_66214_half_map_1.map
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Half map: #2

Fileemd_66214_half_map_2.map
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Sample components

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Entire : Contractile injection system in marine bacterium Algoriphagus mac...

EntireName: Contractile injection system in marine bacterium Algoriphagus machipongonensis
Components
  • Complex: Contractile injection system in marine bacterium Algoriphagus machipongonensis

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Supramolecule #1: Contractile injection system in marine bacterium Algoriphagus mac...

SupramoleculeName: Contractile injection system in marine bacterium Algoriphagus machipongonensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 30251
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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