6XFJ

Crystal structure of the type III secretion pilotin InvH

• PDB DOI:  https://doi.org/10.2210/pdb6XFJ/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2020-06-15 Released: 2020-09-16 
• Deposition Author(s): Majewski, D.D., Okon, M., Heinkel, F., Robb, C.S., Vuckovic, M., McIntosh, L.P., Strynadka, N.C.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.168 
• R-Value Work: 0.132 
• R-Value Observed: 0.134 

Literature

Characterization of the Pilotin-Secretin Complex from the Salmonella enterica Type III Secretion System Using Hybrid Structural Methods.

Majewski, D.D., Okon, M., Heinkel, F., Robb, C.S., Vuckovic, M., McIntosh, L.P., Strynadka, N.C.J.

(2021) Structure 29: 125-138.e5

• PubMed: 32877645 
• DOI: https://doi.org/10.1016/j.str.2020.08.006
• Primary Citation of Related Structures:  
  6XFJ, 6XFK, 6XFL


• PubMed Abstract: 
  

The type III secretion system (T3SS) is a multi-membrane-spanning protein channel used by Gram-negative pathogenic bacteria to secrete effectors directly into the host cell cytoplasm. In the many species reliant on the T3SS for pathogenicity, proper assembly of the outer membrane secretin pore depends on a diverse family of lipoproteins called pilotins. We present structural and biochemical data on the Salmonella enterica pilotin InvH and the S domain of its cognate secretin InvG. Characterization of InvH by X-ray crystallography revealed a dimerized, α-helical pilotin. Size-exclusion-coupled multi-angle light scattering and small-angle X-ray scattering provide supporting evidence for the formation of an InvH homodimer in solution. Structures of the InvH-InvG heterodimeric complex determined by X-ray crystallography and NMR spectroscopy indicate a predominantly hydrophobic interface. Knowledge of the interaction between InvH and InvG brings us closer to understanding the mechanisms by which pilotins assemble the secretin pore.

---

Organizational Affiliation: 

Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 40.27 kDa 
• Atom Count: 3,048 
• Modelled Residue Count: 306 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type 3 secretion system pilotin	A, B, C, D	82	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: invH, sctG, STM2900 Membrane Entity: Yes
UniProt
Find proteins for P0CL43 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0CL43  Go to UniProtKB:  P0CL43

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	AA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], IA [auth D], JA [auth D], KA [auth D], N [auth B], O [auth B], P [auth B], Q [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], LA [auth D], M [auth A], MA [auth D], R [auth B], S [auth B], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	V [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.168 
• R-Value Work: 0.132 
• R-Value Observed: 0.134 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.503	α = 107.69
b = 53.183	β = 97.2
c = 56.851	γ = 95.95

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Majewski, D.D., Okon, M., Heinkel, F., Robb, C.S., Vuckovic, M., McIntosh, L.P., Strynadka, N.C.J.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2021-02-17
  Changes: Database references