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- PDB-9flx: CryoEM structure of the fragment-4 (4074-4421) in the grappling h... -

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Entry
Database: PDB / ID: 9flx
TitleCryoEM structure of the fragment-4 (4074-4421) in the grappling hook protein A (GhpA) in the bacterium Aureispira sp. CCB-QB1
ComponentsThe grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
KeywordsCELL ADHESION / ixotrophy / type 9 secretion system / cryoEM / surface protein / predation
Biological speciesAureispira sp. CCB-QB1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLien, Y.-W. / Amendola, D. / Lee, K.S. / Bartlau, N. / Xu, J. / Furusawa, G. / Polz, M.F. / Stocker, R. / Weiss, G.L. / Pilhofer, M.
Funding support Switzerland, European Union, United States, 6items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_212592 Switzerland
European Research Council (ERC)679209European Union
European Research Council (ERC)101000232European Union
Swiss National Science Foundation315230_176189 Switzerland
Simons Foundation572792 United States
Simons Foundation542395 United States
Citation
Journal: Science / Year: 2024
Title: Mechanism of bacterial predation via ixotrophy.
Authors: Yun-Wei Lien / Davide Amendola / Kang Soo Lee / Nina Bartlau / Jingwei Xu / Go Furusawa / Martin F Polz / Roman Stocker / Gregor L Weiss / Martin Pilhofer /
Abstract: Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be ...Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.
#1: Journal: Biorxiv / Year: 2024
Title: Mechanism of bacterial predation via ixotrophy
Authors: Lien, Y.W. / Amendola, D. / Lee, K.S. / Bartlau, N. / Xu, J. / Furusawa, G. / Polz, M.F. / Stocker, R. / Weiss, G.L. / Pilhofer, M.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
A: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
C: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
D: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
E: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
F: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1
G: The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1


Theoretical massNumber of molelcules
Total (without water)4,270,8017
Polymers4,270,8017
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
The grappling hook protein A in the bacterium Aureispira sp. CCB-QB1


Mass: 610114.375 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Details: The structure covers the amino acid residues 4074-4422 in the GhpA protein.
Source: (natural) Aureispira sp. CCB-QB1 (bacteria)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Crude purification of the grappling hooks from the surface of the bacterium Aureispira sp. CCB-QB1.
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Aureispira sp. CCB-QB1 (bacteria)
Buffer solutionpH: 7.5
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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39561 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0172587
ELECTRON MICROSCOPYf_angle_d1.4733585
ELECTRON MICROSCOPYf_dihedral_angle_d9.342860
ELECTRON MICROSCOPYf_chiral_restr0.075445
ELECTRON MICROSCOPYf_plane_restr0.007465

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