Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module.

Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R, Sci Adv 10(1):eadj2403 (2024) Europe PMC

SASDPM3 – Vibrio cholerae ParD2:ParE2 complex bound to 33-bp DNA operator fragment

Antitoxin ParD
Toxin
33-bp DNA operator fragment
MWexperimental 100 kDa
MWexpected 99 kDa
VPorod 150 nm3
log I(s) 2.89×10-1 2.89×10-2 2.89×10-3 2.89×10-4
Antitoxin ParD Toxin 33-bp DNA operator fragment small angle scattering data  s, nm-1
ln I(s)
Antitoxin ParD Toxin 33-bp DNA operator fragment Guinier plot ln 2.90×10-1 Rg: 3.2 nm 0 (3.2 nm)-2 s2
(sRg)2I(s)/I(0)
Antitoxin ParD Toxin 33-bp DNA operator fragment Kratky plot 1.104 0 √3 sRg
Dmax: 10 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Antitoxin ParD Toxin 33-bp DNA operator fragment CUSTOM IN-HOUSE model
Antitoxin ParD Toxin 33-bp DNA operator fragment CUSTOM IN-HOUSE model
Synchrotron SAXS data from solutions of Vibrio cholerae ParD2:ParE2 complex bound to 33-bp DNA operator fragment in 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH 8 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 10 mg/ml was injected at a 0.75 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 19°C. 480 successive 0.990 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Antitoxin ParD (ParD2)
Mol. type   Protein
Organism   Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Olig. state   Hexamer
Mon. MW   9.0 kDa
 
UniProt   P58093 (1-80)
Sequence   FASTA
 
Toxin (ParE2)
Mol. type   Protein
Organism   Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Olig. state   Other
Mon. MW   12.4 kDa
 
UniProt   Q9KMJ0 (1-99)
Sequence   FASTA
 
33-bp DNA operator fragment (33-bp DNA operator)
Mol. type   DNA
Organism   Vibrio cholerae O1
Olig. state   Monomer
Mon. MW   20.4 kDa
Sequence   FASTA
 
PDB ID   7R5A
 
PDB ID   7R5A