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 4G2S | pdb_00004g2s

Crystal structure of a Salmonella type III secretion system protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.257 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4G2S

This is version 1.1 of the entry. See complete history. 

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

  • 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.

Macromolecule Content 

  • Total Structure Weight: 72.08 kDa 
  • Atom Count: 4,972 
  • Modeled Residue Count: 636 
  • Deposited Residue Count: 666 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein prgH
A, B, C, D, E
A, B, C, D, E, F
111Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: prgH, STM2874
UniProt
Find proteins for P41783 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P41783 
Go to UniProtKB:  P41783
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41783
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.94α = 90
b = 120.58β = 96.7
c = 78.28γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MxDCdata collection
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description