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- PDB-9ezm: CryoEM structure of the contracted sheath in H. borinquense -

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Basic information

Entry
Database: PDB / ID: 9ezm
TitleCryoEM structure of the contracted sheath in H. borinquense
ComponentsPhage tail sheath protein FI
KeywordsSTRUCTURAL PROTEIN / archaea / contractile injection system / sheath / cryoEM
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZachs, T. / Malit, J.J. / Xu, J. / Schuerch, A. / Sivabalasarma, S. / Nussbaum, P. / Albers, S.V. / Pilhofer, M.
Funding support Switzerland, European Union, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage tail sheath protein FI
B: Phage tail sheath protein FI
C: Phage tail sheath protein FI
D: Phage tail sheath protein FI
E: Phage tail sheath protein FI
F: Phage tail sheath protein FI
G: Phage tail sheath protein FI
H: Phage tail sheath protein FI
I: Phage tail sheath protein FI
J: Phage tail sheath protein FI
K: Phage tail sheath protein FI
L: Phage tail sheath protein FI
M: Phage tail sheath protein FI
N: Phage tail sheath protein FI
O: Phage tail sheath protein FI
P: Phage tail sheath protein FI
Q: Phage tail sheath protein FI
R: Phage tail sheath protein FI


Theoretical massNumber of molelcules
Total (without water)1,139,77518
Polymers1,139,77518
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
Phage tail sheath protein FI


Mass: 63320.820 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) Halogeometricum borinquense DSM 11551 (archaea)
References: UniProt: E4NVX6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: The sheath protein of Halogeometricum borinquense / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Halogeometricum borinquense DSM 11551 (archaea)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3300 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 33.24 ° / Axial rise/subunit: 17.09 Å / Axial symmetry: C6
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127891 / Symmetry type: HELICAL

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