Structural characterization of pH-modulated closed and open states in a pentameric ligand-gated ion channel

Marie Lycksell.

SASDVY3 – Desulfofustis sp. PB-SRB1 ligand-gated ion channel DeCLIC without calcium at pH 5 by paused SEC-SANS

Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
MWexperimental 349 kDa
MWexpected 342 kDa
VPorod 558 nm3
log I(s) 3.07×103 3.07×102 3.07×101 3.07×100
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein small angle scattering data  s, nm-1
ln I(s)
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein Guinier plot ln 3.07×103 Rg: 5.2 nm 0 (5.2 nm)-2 s2
(sRg)2I(s)/I(0)
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein Kratky plot 1.104 0 3 sRg
p(r)
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein pair distance distribution function Rg: 5.1 nm 0 Dmax: 18.4 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Desulfofustis sp. PB-SRB1 ligand-gated ion channel DeCLIC without calcium at pH 5 by paused SEC-SANS Rg histogram Rg, nm
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein GROMACS model
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein GROMACS model

log I(s)
 s, nm-1
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein GROMACS model

log I(s)
 s, nm-1
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein GROMACS model

SANS data from solutions of Desulfofustis sp. PB-SRB1 ligand-gated ion channel DeCLIC in 20 mM citrate, 150 mM NaCl, 10 mM EDTA, 0.5 mM deuterated n-Dodecyl-β-D-Maltoside, in 100% v/v D2O, pH 5 were collected on the D22 instrument at the ILL (Grenoble, France) using a Reuter-Stokes 3He detector at a sample-detector distances of 1.4 m and 8 m (measured simultaneously with the D22 dual detector banks) and at a wavelength of λ = 0.6 nm; Δλ/λ = 10% (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 250.00 μl sample at 5.5 mg/ml was injected onto a GE Superdex 200 Increase 10/300 column at 10°C. Data collection was done as a paused-flow SEC-SANS measurement: an initial flow rate of 0.2 ml/min was used, slowed to 0.01 ml/min when the protein peak entered the measuring cell, and paused to 0 ml/min at the peak maximum for the data collection, after which the flow was turned on to pass the remainder of the column volume. 210 successive 30 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.

Paused SEC-SANS.

Neurotransmitter-gated ion-channel ligand-binding domain-containing protein (DeCLIC)
Mol. type   Protein
Organism   Desulfofustis sp. PB-SRB1
Olig. state   Pentamer
Mon. MW   68.4 kDa
 
UniProt   V4JF97 (34-642)
Sequence   FASTA