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- EMDB-66212: CryoEM structure of one tail-fiber connected to the baseplate wed... -

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Basic information

Entry
Database: EMDB / ID: EMD-66212
TitleCryoEM structure of one tail-fiber connected to the baseplate wedge in the contracted AlgoCIS
Map data
Sample
  • Complex: Contractile injection system in marine bacterium Algoriphagus machipongonensis
    • Protein or peptide: PKD domain-containing protein
    • Protein or peptide: The baseplate protein Alg12
KeywordsContractile injection system / CryoEM / marine bacterium / STRUCTURAL PROTEIN
Function / homologyPolycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / Immunoglobulin-like fold / PKD domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesAlgoriphagus machipongonensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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_66212.png

Downloads & links

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Map

FileDownload / File: emd_66212.map.gz / Format: CCP4 / Size: 669.9 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 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
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05266025 - 0.0829387
Average (Standard dev.)0.000031695145 (±0.0009665237)
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_66212_msk_1.map
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Half map: #1

Fileemd_66212_half_map_1.map
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Half map: #2

Fileemd_66212_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
    • Protein or peptide: PKD domain-containing protein
    • Protein or peptide: The baseplate protein Alg12

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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: PKD domain-containing protein

MacromoleculeName: PKD domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 162.412406 KDa
SequenceString: MANKLSTITT QYHTYKVDQV LTHTQLNESI AFFEDQDRLT RVFLNGVGIV CGFKISRPTS TIIRVSQGIG VTTDGDLLKL LREAAEEDS PGLRIVEEFV DYTHFRDFND ENSHYEKFNL GESKINLWEL VPKEKANETD QPISQIGGLV DKIAVLYLET Y AREADLCS ...String:
MANKLSTITT QYHTYKVDQV LTHTQLNESI AFFEDQDRLT RVFLNGVGIV CGFKISRPTS TIIRVSQGIG VTTDGDLLKL LREAAEEDS PGLRIVEEFV DYTHFRDFND ENSHYEKFNL GESKINLWEL VPKEKANETD QPISQIGGLV DKIAVLYLET Y AREADLCS GINCDNQGVE QVAHLRVLLT DVAGAKHLLA DDGVYQKLDI KTLYGKLKKV KLQKVLLSKA NTKDLQKLED SY YSAIMGA DIGKLSDGLN SISEFLGVNV NVEQALKIFQ QKPSSTYVNF FQYQYDWLRD VISTYHEIIE TLFKLNATCL PDI NAFPKH LMLGRVIPSV GTEQYRHGFY SSPITGDTSV TNKLHLLLER LRLILSTFHT PVTDINITPS VFSGDLGDKA IPFY YKANS VLLNNWSFEK SRMGFNSDIT SYVRQKDEET GITIEPLEID TDENDFYRIE GHQGQGFEKA MIEIQDLVYK YNLDF DVKA VSINEALDSI RMEDYKCHFE DLMVLLDAWN DEISCVTGKI TSFFTSLKIK ELLEENAAAE SESEVASIKE TSKVYQ PTS KSDTMTLEQL AILIKNQKIT LAEAKRLYPY LFESTQDYKT ENSKSIRESV IKNVKEEEES LGFVFQPVFT AEMPVYY GY NEIKVEAEKE VANYLKDFQI QEDEKVALVD KPIEIIAASY DISNYIPERL FELDSGYIVE YETSIESLCE KLDEFSKR V EKLSINDRLK SSLQSRALYF TSVCCAANKL KILQAEIEAR KKHILEQLQF SNFHEHHPGL DHRAGVSKGG TFVMVYYTR PTRVSKRGIS IAGFKEISVA ENSYGDFSKT IDLNEISKEL NLFTDPKNLE KDLEIFRKQL SGDKSSLHGL DVLKSRNLKS NLKDKTVIA DFMLPYRCCS DCNPINFIVP RPVIFLNLNT ETYCLGLEQE EISFEVIPVD GEVTVVDNVA GVIISGRSIS I DPGAFPKE MLGEAISFLV NDEPTDAKLT VLQAPTFVLN LPDGPVSDPS IEFSASPSFD NAGYLWEFGD GTSSTEVAPK KT FSLPVNA ENKISVSLTI TPENGACPNR VTGEIVFEEQ EEEVDLTLTP NEFCRDQSTE PVAFGVVPDD GNVTGPGVQP GEN GNGFVF NPILIEDIDL EKDLRFRVNG KETDLIVRVY QTPVIAFTTS AVNNPTNNSK TVTLTITNPP SSVREYIWSI NDKD RAGTS ESSYTETFPA SVTSLKVSVL AILSNLCEEA SSNVSIIILQ SGSVDTCTDI GEKWLSDQNL RISRFMESPD FEKID DWGQ QTYTQAINGI KNDNGADIIG FAEIVKNSSL YLAGGDEQNK QLMQIFSNHY PPLISYIMEM NSNNGPGVLP MKDLYK TFV QLFYTLIRCQ DKEVLIERGA EFQFDAIVSR ITSDFKELQG SSIKWDVNDE IPGIYEELLE VFDSVPYLKN GLQNQLT LM V

UniProtKB: PKD domain-containing protein

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Macromolecule #2: The baseplate protein Alg12

MacromoleculeName: The baseplate protein Alg12 / type: protein_or_peptide / ID: 2
Details: Note that the residues between 663 and 716 are missing, mainly due to the poor map density.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 106.550484 KDa
SequenceString: MSSKDDLDFH FLREEGIRYI KELGSNFWTD YNTHDPGITM LEVLCYAISD LGNRINIPIE DLIANEEGGV KGQFYKVQEI LPSAPTSEL DLRKLFIDIE GIKNCWIKRE RVTVFADLKN QKLSYEKTIW EDLKENQKAQ FDLKGLYRIL VETEDADKVL S ESLEKAVF ...String:
MSSKDDLDFH FLREEGIRYI KELGSNFWTD YNTHDPGITM LEVLCYAISD LGNRINIPIE DLIANEEGGV KGQFYKVQEI LPSAPTSEL DLRKLFIDIE GIKNCWIKRE RVTVFADLKN QKLSYEKTIW EDLKENQKAQ FDLKGLYRIL VETEDADKVL S ESLEKAVF TKFHANRNLC EDLIKVEKVA TEPISVCANV EVAPEADEEL IHAQILIAIE DYLAPSPRHY SLKQMVDKGY TM DEIFEGP FLENGFIDTV ELKASELRKE VRLSDIINII MSIDGVKIVK EITLGNCDEN DGIENNQWVI CIPENKKPKL CKK TTINYF KGILPINLNP VRVDNHKSKI LASRLENDLK AKDDLEPAIP QGTFADWGEY SSIQHEFPET YGISDIGLPP KLGV KRAVL ARQLKGYLLF FDQILASYFE HLSKIKSLLS LDQGPSFTYF TQAIKDIKDV EELFKDPTLL ENDEELTKSL IGKLD DTIE RRNQLMDHLI ARFAENFSSY AFLMKFLYGE STDEIVLQDK QSFLREYKEI SRERGEGFNF YEQSNDNLWD TLNVSG AQK RISKLVGVKD YSRRNLSDTA VEIYRYEHVD GNWVYRWRIR DENGKVLLSA TTSYPTYNSA GNEMYFAILK ILETPLS DL EKLLEVNFRN ENEAGSFHFH KAATSNKFSF DIINPVIDSE SSSDFIVAKQ YTYYPDRTQA VLGAISLLNF IKYTFTFT E EGIYLVEHIL LRPSPLDPEY LAMQTDAGKE YIEGNFLPFC SDDYENCKMI DPYSFRVSIV LPGFTYRFAN KDFRDYLEN LIREELPAHI VAKICWIGYR KGEEPELFQE DVENPETPIF KENQLEIFEK AYKNYLFELT DIHKRKGFIA SMNKYNQVLN EMTSSLTGL HTIYPTGRLY DCEDEEEELD GKLILGKTNL GTL

UniProtKB: Uncharacterized 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:

11748

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 72307
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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