Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.89 kDa 
• Atom Count: 4143 
• Modelled Residue Count: 524 
• Deposited Residue Count: 610 
• Unique protein chains: 1

3ZQE

PrgI-SipD from Salmonella typhimurium in complex with deoxycholate

• PDB DOI: 10.2210/pdb3ZQE/pdb

• Classification: CELL INVASION
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 21829362 
• DOI: 10.1371/journal.ppat.1002163
• Primary Citation of Related Structures:  
  2YM0, 2YM9, 3ZQB, 3ZQE


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN PRGI, CELL INVASION PROTEIN SIPD	A, B	305	Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344	Mutation(s): 0
UniProt
Find proteins for P41784 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P41784  Go to UniProtKB:  P41784
Find proteins for Q56026 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q56026  Go to UniProtKB:  Q56026
UniProt Groups	P41784Q56026

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DXC	E [auth B]	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID C24 H40 O4 KXGVEGMKQFWNSR-LLQZFEROSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DXC	PDBBind:  3ZQE	Kd: 5.90e+4 (nM) from 1 assay(s)
	Binding MOAD:  3ZQE	Kd: 5.90e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.284 
• R-Value Work: 0.246 
• R-Value Observed: 0.246 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.152	α = 90
b = 47.456	β = 121.96
c = 102.627	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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
  Changes: Other