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- EMDB-66213: CryoEM structure of cap module in the contracted AlgoCIS -

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Basic information

Entry
Database: EMDB / ID: EMD-66213
TitleCryoEM structure of cap module in the contracted AlgoCIS
Map data
Sample
  • Complex: Contractile injection system in marine bacterium Algoriphagus machipongonensis
    • Protein or peptide: Pvc16 N-terminal domain-containing protein
    • Protein or peptide: Putative phage tail sheath protein FI
    • Protein or peptide: Phage tail protein
KeywordsContractile injection system / CryoEM / marine bacterium / STRUCTURAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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

emd_66213.png

Downloads & links

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Map

FileDownload / File: emd_66213.map.gz / Format: CCP4 / Size: 178 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.)
1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.08812034 - 0.11570172
Average (Standard dev.)0.0003328068 (±0.0044997567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66213_msk_1.map
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Half map: #2

Fileemd_66213_half_map_1.map
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Half map: #1

Fileemd_66213_half_map_2.map
Projections & Slices
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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
    • Protein or peptide: Pvc16 N-terminal domain-containing protein
    • Protein or peptide: Putative phage tail sheath protein FI
    • Protein or peptide: Phage tail protein

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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: all
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)

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

MacromoleculeName: Pvc16 N-terminal domain-containing protein / type: protein_or_peptide / ID: 1
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.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 22.868871 KDa
SequenceString: MIFEVLKILT DEVNQNFKGL EMEDSEVVLN NVALIDSQQD VATELQNKVI LSMINLREEV TMKNFPNNVL EGTKVTYKNP KNNINLFLI FCANRTGYKK SLSDLSRILE FFQHKSVFTQ SNTSFDRDLE EMENVKNFRF TMELFTPTFE ELNYIWGTLG G RQYPSVFY ...String:
MIFEVLKILT DEVNQNFKGL EMEDSEVVLN NVALIDSQQD VATELQNKVI LSMINLREEV TMKNFPNNVL EGTKVTYKNP KNNINLFLI FCANRTGYKK SLSDLSRILE FFQHKSVFTQ SNTSFDRDLE EMENVKNFRF TMELFTPTFE ELNYIWGTLG G RQYPSVFY KLNLIVIDRD ATTSEEGVIT NIHRNYET

UniProtKB: Pvc16 N-terminal domain-containing protein

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Macromolecule #2: Putative phage tail sheath protein FI

MacromoleculeName: Putative phage tail sheath protein FI / type: protein_or_peptide / ID: 2
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.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 76.319039 KDa
SequenceString: MATYKTPGVY IEEITKFPPS VAQVETAIPA FIGYTQFART KPSVDSDDLI LKPKRISSLL DFTTYYGGAQ NEQGITVKLT DTLIEGAEN RTINVPEPTF KSPYLMFYSL QMYFANGGGP CYIVSTGVYD DWSDSETPPT INFSDLESGL AVIRKEDEPT L LLFPDATN ...String:
MATYKTPGVY IEEITKFPPS VAQVETAIPA FIGYTQFART KPSVDSDDLI LKPKRISSLL DFTTYYGGAQ NEQGITVKLT DTLIEGAEN RTINVPEPTF KSPYLMFYSL QMYFANGGGP CYIVSTGVYD DWSDSETPPT INFSDLESGL AVIRKEDEPT L LLFPDATN LPTDDEFYSL YNSALMQCND LQDRFTILDT YSDQTYNDGV EDLDPIPALR NGINLTKDYL KYGAAYYPFV QT ILNYQYS ADEIVIQHLS YNPNAIATAL DNLNAVNGPT FIDAILDDLR DLSLPDISGE ISDAVGFMYD DVDGFDIDGT FTT NSVKVA NFASLVESVL STLNELIDAK EEINKDVNSA IASSEEDNAI KTAISDALDV FNEDFEGADK IESVAKNLSD LLIK IKQAD TNTKVENVLS INALNFSAEF EKLLTYDVNT GLTASVTLDL FANIGTRLDD IIAAVSAAEP IDVNNGKLNG RLLSD IEPL DNATYNTILL EINSHKVTLP PSSSMAGAYA RVDNDRGVWK SPANIGLNYV SKPSVTVSHE EQESMNVHGT GKSVNA IRS FVGKGTLVWG ARTLAGNDNE WRYISVRRFF NMAEESIKKA TEQFVFEPND GNTWVRVRAM IENFLILQWR AGALAGA KP EHAFYVKVGL GQTMTAQDIL EGNMNVEIGL AVVRPAEFII LKFSHKMQES

UniProtKB: Phage tail sheath protein FI

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Macromolecule #3: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 16.375458 KDa
SequenceString:
MSYPLSKFHF SVEWGGTKIG FTEVSGLDLE TEIIEYRHGA SPEYSKIKMP GMQKFSNITL KRGTFKSDNE YFQWYNTINL NKVERRDLT ISLLNEEHEP VVTWKVKNAW PLKVQSTDLK GDGNEVAIES MELAHEGLVI QNE

UniProtKB: Phage tail protein

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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:

11734

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 12926
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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