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- PDB-9wsz: CryoEM structure of baseplate iris structure in the contracted AlgoCIS -

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Basic information

Entry
Database: PDB / ID: 9wsz
TitleCryoEM structure of baseplate iris structure in the contracted AlgoCIS
Components
  • Baseplate protein Alg12
  • Baseplate protein J-like domain-containing protein
KeywordsSTRUCTURAL PROTEIN / Contractile injection system / CryoEM / marine bacterium
Function / homologyUncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesAlgoriphagus machipongonensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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
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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: Baseplate protein Alg12
G: Baseplate protein J-like domain-containing protein
B: Baseplate protein Alg12
H: Baseplate protein J-like domain-containing protein
C: Baseplate protein Alg12
I: Baseplate protein J-like domain-containing protein
D: Baseplate protein Alg12
J: Baseplate protein J-like domain-containing protein
E: Baseplate protein Alg12
K: Baseplate protein J-like domain-containing protein
F: Baseplate protein Alg12
L: Baseplate protein J-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)1,355,57912
Polymers1,355,57912
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
Baseplate protein Alg12


Mass: 106550.484 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: Please note that the region (663-716aa) is missing in the deposit structure due to the poor map density.
Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTB3
#2: Protein
Baseplate protein J-like domain-containing protein


Mass: 119379.320 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTB4
Has protein modificationY

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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
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30251 / Symmetry type: POINT

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