3J1X | pdb_00003j1x

A refined model of the prototypical Salmonella typhimurium T3SS basal body reveals the molecular basis for its assembly

• PDB DOI: https://doi.org/10.2210/pdb3J1X/pdb
• EM Map EMD-1875: EMDB EMDataResource

• Classification: CELL INVASION
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Mutation(s): No 


• Deposited: 2012-07-10 Released: 2013-05-22 
• Deposition Author(s): Sgourakis, N.G., Bergeron, J.R.C., Worrall, L.J., Strynadka, N.C.J., Baker, D.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 11.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly.

Bergeron, J.R., Worrall, L.J., Sgourakis, N.G., Dimaio, F., Pfuetzner, R.A., Felise, H.B., Vuckovic, M., Yu, A.C., Miller, S.I., Baker, D., Strynadka, N.C.

(2013) PLoS Pathog 9: e1003307-e1003307

• PubMed: 23633951 
• DOI: https://doi.org/10.1371/journal.ppat.1003307
• Primary Citation Related Structures: 
  3J1V, 3J1W, 3J1X, 4G08, 4G1I, 4G2S


• PubMed Abstract: 
  

  The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a "basal body", a lock-nut structure spanning both bacterial membranes, and a "needle" that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C24  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 537.2 kDa 
• Atom Count: 37,896 
• Modeled Residue Count: 4,584 
• Deposited Residue Count: 4,584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PrgH	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	191	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0
UniProt
Find proteins for P41783 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P41783  Go to UniProtKB:  P41783

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 11.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	IMAGIC

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Sgourakis, N.G., Bergeron, J.R.C., Worrall, L.J., Strynadka, N.C.J., Baker, D.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Refinement description