Molecular model of a sensor of two-component signaling system

Ryzhykau Y, Orekhov P, Rulev M, Vlasov A, Melnikov I, Volkov D, Nikolaev M, Zabelskii D, Murugova T, Chupin V, Rogachev A, Gruzinov A, Svergun D, Brennich M, Gushchin I, Soler-Lopez M, Bothe A, Büldt G, Leonard G, Engelhard M, Kuklin A, Gordeliy V, Scientific Reports 11(1) (2021) DOI

SASDK27 – SAXS data for the sensory rhodopsin II / transducer complex in detergent at 0.15 M NaCl

Sensory rhodopsin II from Natronbacterium pharaonis
Sensory rhodopsin II transducer from Natronomonas pharaonis
MWexperimental 311 kDa
MWexpected 169 kDa
log I(s) 1.28×10-1 1.28×10-2 1.28×10-3 1.28×10-4
Sensory rhodopsin II from Natronbacterium pharaonis Sensory rhodopsin II transducer from Natronomonas pharaonis small angle scattering data  s, nm-1
ln I(s)
Sensory rhodopsin II from Natronbacterium pharaonis Sensory rhodopsin II transducer from Natronomonas pharaonis Guinier plot ln 1.28×10-1 Rg: 9.0 nm 0 (9.0 nm)-2 s2
(sRg)2I(s)/I(0)
Sensory rhodopsin II from Natronbacterium pharaonis Sensory rhodopsin II transducer from Natronomonas pharaonis Kratky plot 1.104 0 √3 sRg
p(r)
Sensory rhodopsin II from Natronbacterium pharaonis Sensory rhodopsin II transducer from Natronomonas pharaonis pair distance distribution function Rg: 9.8 nm 0 Dmax: 38.9 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Sensory rhodopsin II from Natronbacterium pharaonis Sensory rhodopsin II transducer from Natronomonas pharaonis MEMPROT model
log I(s)
 s, nm-1
Sensory rhodopsin II from Natronbacterium pharaonis Sensory rhodopsin II transducer from Natronomonas pharaonis OTHER [STATIC IMAGE] model
Synchrotron SAXS data from solutions of the sensory rhodopsin II / transducer complex in 150 mM NaCl, 25 mM Na/Na-Pi, 1.0 mM EDTA, 0.05% DDM, pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09918 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.57 mg/ml was measured at 4°C. 14 successive 0.500 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.

The protein of study is a non-fused complex of sensory rhodopsin II (NpSRII, UniProt ID P42196) with its cognate transducer (NpHtrII, UniProt ID P42259) from Nartonomonas pharaonis. The NpSRII/NpHtrII complex in 0.05% (w/v) n-Dodecyl β-D-maltoside (DDM) detergent forms dimers at 150 mM NaCl. For the "straight" model of the NpSRII/NpHtrII dimer, chi-square of the fit is 5.1. Taking into account possible conformational flexibility associated with the HAMP1, HAMP2 and Gly flexible hinges, the chi-square value can be reduced to 3.4.

Sensory rhodopsin II from Natronbacterium pharaonis (NpSRII)
Mol. type   Protein
Organism   Natronomonas pharaonis
Olig. state   Dimer
Mon. MW   26.7 kDa
 
UniProt   P42196 (1-239)
Sequence   FASTA
 
Sensory rhodopsin II transducer from Natronomonas pharaonis (NpHtrII)
Mol. type   Protein
Organism   Natronomonas pharaonis
Olig. state   Dimer
Mon. MW   57.8 kDa
 
UniProt   P42259 (3-534)
Sequence   FASTA