3ZQE

PrgI-SipD from Salmonella typhimurium in complex with deoxycholate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


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

Literature

Crystal Structure of Prgi-Sipd: Insight Into a Secretion Competent State of the Type Three Secretion System Needle Tip and its Interaction with Host Ligands

Lunelli, M., Hurwitz, R., Lambers, J., Kolbe, M.

(2011) Plos Pathog. 7: 02163

  • DOI: 10.1371/journal.ppat.1002163
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Many infectious gram-negative bacteria, including Salmonella typhimurium, require a Type Three Secretion System (T3SS) to translocate virulence factors into host cells. The T3SS consists of a membrane protein complex and an extracellular needle toget ...

    Many infectious gram-negative bacteria, including Salmonella typhimurium, require a Type Three Secretion System (T3SS) to translocate virulence factors into host cells. The T3SS consists of a membrane protein complex and an extracellular needle together that form a continuous channel. Regulated secretion of virulence factors requires the presence of SipD at the T3SS needle tip in S. typhimurium. Here we report three-dimensional structures of individual SipD, SipD in fusion with the needle subunit PrgI, and of SipD:PrgI in complex with the bile salt, deoxycholate. Assembly of the complex involves major conformational changes in both SipD and PrgI. This rearrangement is mediated via a π bulge in the central SipD helix and is stabilized by conserved amino acids that may allow for specificity in the assembly and composition of the tip proteins. Five copies each of the needle subunit PrgI and SipD form the T3SS needle tip complex. Using surface plasmon resonance spectroscopy and crystal structure analysis we found that the T3SS needle tip complex binds deoxycholate with micromolar affinity via a cleft formed at the SipD:PrgI interface. In the structure-based three-dimensional model of the T3SS needle tip, the bound deoxycholate faces the host membrane. Recently, binding of SipD with bile salts present in the gut was shown to impede bacterial infection. Binding of bile salts to the SipD:PrgI interface in this particular arrangement may thus inhibit the T3SS function. The structures presented in this study provide insight into the open state of the T3SS needle tip. Our findings present the atomic details of the T3SS arrangement occurring at the pathogen-host interface.

    Organizational Affiliation: 

    Max Planck Institute for Infection Biology, Department of Cellular Microbiology, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN PRGI, CELL INVASION PROTEIN SIPD
A, B
305Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: prgI, sipD (sspD)
Find proteins for P41784 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P41784
Find proteins for Q56026 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q56026
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DXC
Query on DXC
Download SDF File 
Download CCD File 
B
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
DEOXYCHOLIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DXCKd: 59000 nM BINDINGMOAD
DXCKd: 59000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 171.152α = 90.00
b = 47.456β = 121.96
c = 102.627γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-06-09 
  • Released Date: 2011-08-17 
  • Deposition Author(s): Lunelli, M., Kolbe, M.

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Other