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- EMDB-66211: CryoEM structure of baseplate iris structure in the contracted AlgoCIS -

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Basic information

Entry
Database: EMDB / ID: EMD-66211
TitleCryoEM structure of baseplate iris structure in the contracted AlgoCIS
Map data
Sample
  • Complex: Contractile injection system in marine bacterium Algoriphagus machipongonensis
    • Protein or peptide: Baseplate protein Alg12
    • Protein or peptide: Baseplate protein J-like domain-containing protein
KeywordsContractile injection system / CryoEM / marine bacterium / STRUCTURAL PROTEIN
Function / homologyUncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesAlgoriphagus machipongonensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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_66211.png

Downloads & links

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Map

FileDownload / File: emd_66211.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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 (log scale)
Contour LevelBy AUTHOR: 0.0115
Minimum - Maximum-0.036688875 - 0.05611709
Average (Standard dev.)0.0001226104 (±0.0012399467)
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_66211_msk_1.map
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Half map: #2

Fileemd_66211_half_map_1.map
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Half map: #1

Fileemd_66211_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: Baseplate protein Alg12
    • Protein or peptide: Baseplate protein J-like domain-containing 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: Baseplate protein Alg12

MacromoleculeName: Baseplate protein Alg12 / type: protein_or_peptide / ID: 1
Details: Please note that the region (663-716aa) is missing in the deposit structure due to the poor map density.
Number of copies: 6 / 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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Macromolecule #2: Baseplate protein J-like domain-containing protein

MacromoleculeName: Baseplate protein J-like domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)
Molecular weightTheoretical: 119.37932 KDa
SequenceString: MSENCNHIVT TLKRDGTGRR DLLDPKLAPE SVQLQDFELS DWLIFALNFA RKIHFFPSDL ANEPLGDWRN FFSTIVSDKT LISDIENLD DFEKLRGNIE EFLAAYDQSG KLTPHLTLFV SFLKLLETSK KRFNQLTKRH LDFYYQEILH LEKQALSPDH V FLIFELAK ...String:
MSENCNHIVT TLKRDGTGRR DLLDPKLAPE SVQLQDFELS DWLIFALNFA RKIHFFPSDL ANEPLGDWRN FFSTIVSDKT LISDIENLD DFEKLRGNIE EFLAAYDQSG KLTPHLTLFV SFLKLLETSK KRFNQLTKRH LDFYYQEILH LEKQALSPDH V FLIFELAK NVSQEKLDEG TEVDGGKDDT GKKNTYLTSF ETVLNKTKVG QLKSLYNEIS VEKEEIKELN TPISTGTFVM AP MANSFDG LGEDFPKGSE KWWPFGYTKI CNASTVLPAL PKARLGCSIS SKLLKLSEGT RDIILEFTFN KPILPNGEDY TAL NKAMSI ELTGEKGWIA GLPMTLKSDS GINSGSKKMK LSLTLDSEQP AVVPYQTELH EGSYEVDEPL LRVLFKTNEK EGYN LYRLF NENVLTDLKI TVEVSDITSV QLENDLGVLN PQKPFFPFGP RPIKGSSFIV KYPEAMEKPV TAISYQMDYL NLPEN LVNH YSAYTIGDDE PLVSDMDYFS VKSFPKSSND SDQLFSEKSG GGYESDFEFQ IENGVWESGL KKELKISLER SFLHEK YAH YFTLVAISKD TDPTIELLPN EPYAPLAENL VLGYTAISSI DFSSSSSENQ VSLIHEMPFG FQQVFTPGDT DNSLYLV PD YCHGGELYIG LENGKNLQQV TLLLQFLEGS ENPDITDIFT GNQKIKWQYL SQNQWQDFQS GEIIQNQTPR FLKSGIFQ F SIPKQANLDN TVLPPGYHWI KASMVKPFDV VSQLINIHAQ AVEAVFEDQG SSGNHLEKGL PAETISKLQE RLSWIKSIQ QPYPSTKGKA QESDEDYYRR VSERLRHKKR AITLWDYEHL ILQKFPKVYK VKCLNHTCSS SFQSPGNATL ILVPDTVQQS VFDIYQPRV SQGTLNDVAA FVNELNSFHV QAKVINPNYE EVKVDVKVKF REGLDVSFYL TKVKEDIKKF LSPWAYDQES S VEFGVTLH RSQMIHYLEQ LTYVDYITDL RLLKRQAGSS PCNPIFIETT EKEYIQPSNP KSILVSAKEH LVTPITQNCS SI SLNNEEE CQH

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: 3.7 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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