4G1I

Structure of the PrgH periplasmic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1371/journal.ppat.1003307
  • Primary Citation of Related Structures:  

  • 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 bo ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein prgH
A, B
227Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: prgH
Find proteins for P41783 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P41783
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A, B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 264.432α = 90.00
b = 33.380β = 91.60
c = 48.530γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
MxDCdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description