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- PDB-9wt1: CryoEM structure of cap module in the contracted AlgoCIS -

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Basic information

Entry
Database: PDB / ID: 9wt1
TitleCryoEM structure of cap module in the contracted AlgoCIS
Components
  • Phage tail protein
  • Putative phage tail sheath protein FI
  • Pvc16 N-terminal domain-containing protein
KeywordsSTRUCTURAL PROTEIN / Contractile injection system / CryoEM / marine bacterium
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Phage tail protein / Phage tail sheath protein FI / Pvc16 N-terminal domain-containing protein
Similarity search - Component
Biological speciesAlgoriphagus machipongonensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXu, J. / Ericson, C.F. / Toenshoff, E.R. / Pilhofer, M.
Funding support Switzerland, European Union, 4items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pvc16 N-terminal domain-containing protein
1A: Putative phage tail sheath protein FI
2A: Putative phage tail sheath protein FI
1a: Phage tail protein
2a: Phage tail protein
B: Pvc16 N-terminal domain-containing protein
1B: Putative phage tail sheath protein FI
2B: Putative phage tail sheath protein FI
1b: Phage tail protein
2b: Phage tail protein
C: Pvc16 N-terminal domain-containing protein
1C: Putative phage tail sheath protein FI
2C: Putative phage tail sheath protein FI
1c: Phage tail protein
2c: Phage tail protein
D: Pvc16 N-terminal domain-containing protein
1D: Putative phage tail sheath protein FI
2D: Putative phage tail sheath protein FI
1d: Phage tail protein
2d: Phage tail protein
E: Pvc16 N-terminal domain-containing protein
1E: Putative phage tail sheath protein FI
2E: Putative phage tail sheath protein FI
1e: Phage tail protein
2e: Phage tail protein
F: Pvc16 N-terminal domain-containing protein
1F: Putative phage tail sheath protein FI
2F: Putative phage tail sheath protein FI
1f: Phage tail protein
2f: Phage tail protein


Theoretical massNumber of molelcules
Total (without water)1,249,54730
Polymers1,249,54730
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Pvc16 N-terminal domain-containing protein


Mass: 22868.871 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: Please note that the region (174-181aa) is replaced by poly-Ala and the region (70-77aa) is missing, mainly due to the poor map density.
Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC4
#2: Protein
Putative phage tail sheath protein FI


Mass: 76319.039 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Details: Please note that the region (260-468aa) is built based on Alphafold predicted structure but only shown as poly-Ala, mainly due to the poor density.
Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC2
#3: Protein
Phage tail protein


Mass: 16375.458 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC1
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Contractile injection system in marine bacterium Algoriphagus machipongonensis
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12926 / Symmetry type: POINT

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