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- EMDB-50089: CryoEM structure of the contracted sheath in H. borinquense -

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Basic information

Entry
Database: EMDB / ID: EMD-50089
TitleCryoEM structure of the contracted sheath in H. borinquense
Map data
Sample
  • Complex: The sheath protein of Halogeometricum borinquense
    • Protein or peptide: Phage tail sheath protein FI
Keywordsarchaea / contractile injection system / sheath / cryoEM / STRUCTURAL PROTEIN
Function / homology: / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Phage tail sheath protein FI
Function and homology information
Biological speciesHalogeometricum borinquense DSM 11551 (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZachs T / Malit JJ / Xu J / Schuerch A / Sivabalasarma S / Nussbaum P / Albers SV / Pilhofer M
Funding support Switzerland, European Union, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_212592 Switzerland
European Research Council (ERC)679209/101000232European Union
CitationJournal: Sci Adv / Year: 2024
Title: Archaeal type six secretion system mediates contact-dependent antagonism.
Authors: Tobias Zachs / Jessie James L Malit / Jingwei Xu / Alexandra Schürch / Shamphavi Sivabalasarma / Phillip Nußbaum / Sonja-Verena Albers / Martin Pilhofer /
Abstract: Microbial communities are shaped by cell-cell interactions. Although archaea are often found in associations with other microorganisms, the mechanisms structuring these communities are poorly ...Microbial communities are shaped by cell-cell interactions. Although archaea are often found in associations with other microorganisms, the mechanisms structuring these communities are poorly understood. Here, we report on the structure and function of haloarchaeal contractile injection systems (CISs). Using a combination of functional assays and time-lapse imaging, we show that exhibits antagonism toward by inducing cell lysis and inhibiting proliferation. This antagonism is contact-dependent and requires a functional CIS, which is encoded by a gene cluster that is associated with toxin-immunity pairs. Cryo-focused ion beam milling and imaging by cryo-electron tomography revealed that these CISs are bound to the cytoplasmic membrane, resembling the bacterial type six secretion systems (T6SSs). We show that related T6SS gene clusters are conserved and expressed in other haloarchaeal strains, which exhibit antagonistic behavior. Our data provide a mechanistic framework for understanding how archaea may shape microbial communities and affect the food webs they inhabit.
History
DepositionApr 12, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50089.png

Downloads & links

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Map

FileDownload / File: emd_50089.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. 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-0.06532303 - 0.10865609
Average (Standard dev.)0.0012309289 (±0.006998095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50089_msk_1.map
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Half map: #2

Fileemd_50089_half_map_1.map
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Half map: #1

Fileemd_50089_half_map_2.map
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Sample components

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Entire : The sheath protein of Halogeometricum borinquense

EntireName: The sheath protein of Halogeometricum borinquense
Components
  • Complex: The sheath protein of Halogeometricum borinquense
    • Protein or peptide: Phage tail sheath protein FI

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Supramolecule #1: The sheath protein of Halogeometricum borinquense

SupramoleculeName: The sheath protein of Halogeometricum borinquense / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halogeometricum borinquense DSM 11551 (archaea)

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Macromolecule #1: Phage tail sheath protein FI

MacromoleculeName: Phage tail sheath protein FI / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Halogeometricum borinquense DSM 11551 (archaea)
Molecular weightTheoretical: 63.32082 KDa
SequenceString: MSEYQSPGVY VEEVQSGSKS VEGVSTSTAG FLGQTERGPV EPRLVTNYAD FERLYGASPK SSDLDAAVDG FFKNGGSRCF IGRVSGADI DDVATGILAD DEGNEIAEVE ANGPGQWGES VAVIVEDSQY PNQFDITVRY WSGDLEAVSK PHGDRPDPSP D VEEVYDGL ...String:
MSEYQSPGVY VEEVQSGSKS VEGVSTSTAG FLGQTERGPV EPRLVTNYAD FERLYGASPK SSDLDAAVDG FFKNGGSRCF IGRVSGADI DDVATGILAD DEGNEIAEVE ANGPGQWGES VAVIVEDSQY PNQFDITVRY WSGDLEAVSK PHGDRPDPSP D VEEVYDGL SADPEASNFY EKQLESSVLV DIEYKDDGTP VDGLTWLHRD SHPTAYSDGG LVETDEEETV VHIPEDLDEL EQ ESLEGIA EPLEIEIDED ADKDDLVVEL EEVREGERDV DVEIVTEKPE ADGEVTLKDY EGVNKPGLRT GLAGFKAIDE ISM VCAPDE NDIDGLTDSI VAHCENMGDR FAILQSPQNP GPVSEMETPV DSSYAAYYYP WVNVLDPVTN REKLVPPGGH IAGI YSRTD QEHGVHKAPA NETLRGIVGL QHNITKGEQD VLNPKGINCI RSFQGRGIRV WGARTTSSDP EWKYLNVRRL FLFIE QSIQ EGTQWAVFEP NEQDTWGRIR QSVTNFLRTV WRNGGLQGQS EDDAFYVKCG EETMSEDDID NGRLIVEIGV APVKPA EFV IFRISQDTEQ A

UniProtKB: Phage tail sheath protein FI

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 17.09 Å
Applied symmetry - Helical parameters - Δ&Phi: 33.24 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127891
Startup modelType of model: EMDB MAP
EMDB ID:

11747

Final angle assignmentType: NOT APPLICABLE

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