9G8B | pdb_00009g8b

CryoEM structure of the fragment-2 (2892-3236) in the grappling hook protein A (GhpA) in the bacterium Aureispira sp. CCB-QB1

• PDB DOI: https://doi.org/10.2210/pdb9G8B/pdb
• EM Map EMD-51127: EMDB EMDataResource

• Classification: CELL ADHESION
• Organism(s): Aureispira sp. CCB-QB1
• Mutation(s): No 


• Deposited: 2024-07-23 Released: 2024-10-16 
• Deposition Author(s): Lien, Y.-W., Amendola, D., Lee, K.S., Bartlau, N., Xu, J., Furusawa, G., Polz, M.F., Stocker, R., Weiss, G.L., Pilhofer, M.
• Funding Organization(s): Swiss National Science Foundation, European Research Council (ERC), Simons Foundation

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of bacterial predation via ixotrophy.

Lien, Y.W., Amendola, D., Lee, K.S., Bartlau, N., Xu, J., Furusawa, G., Polz, M.F., Stocker, R., Weiss, G.L., Pilhofer, M.

(2024) Science 386: eadp0614-eadp0614

• PubMed: 39418385 
• DOI: https://doi.org/10.1126/science.adp0614
• Primary Citation of Related Structures:  
  9FLP, 9FLS, 9FLU, 9FLV, 9FLW, 9FLX, 9FLY, 9G8B


• PubMed 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 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.

---

Organizational Affiliation: 

Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 4,270.8 kDa 
• Atom Count: 17,346 
• Modeled Residue Count: 2,415 
• Deposited Residue Count: 41,286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
The grappling hook protein A (GhpA) in the bacterium Aureispira sp. CCB-QB1	A, B, C, D, E, F, G	5,898	Aureispira sp. CCB-QB1	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Lien, Y.-W., Amendola, D., Lee, K.S., Bartlau, N., Xu, J., Furusawa, G., Polz, M.F., Stocker, R., Weiss, G.L., Pilhofer, M.

---

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_212592
European Research Council (ERC)	European Union	679209
European Research Council (ERC)	European Union	101000232
Swiss National Science Foundation	Switzerland	315230_176189
Simons Foundation	United States	572792
Simons Foundation	United States	542395

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references