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

SASDK67 – SANS data for the sensory rhodopsin II / transducer complex in detergent at 4.0 M NaCl

Sensory rhodopsin II from Natronbacterium pharaonis
Sensory rhodopsin II transducer from Natronomonas pharaonis
MWexperimental 303 kDa
MWexpected 169 kDa
log I(s) 3.18×100 3.18×10-1 3.18×10-2 3.18×10-3
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 3.19×100 Rg: 8.9 nm 0 (8.9 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: 10.9 nm 0 Dmax: 39 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
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 MEMPROT model
Sensory rhodopsin II from Natronbacterium pharaonis Sensory rhodopsin II transducer from Natronomonas pharaonis MEMPROT model
SANS data from solutions of the sensory rhodopsin II / transducer complex in 4000 mM NaCl, 100 mM Na/Na-Pi, 1.0 mM EDTA, 0.05% DDM (D2O buffer), pD 8 were collected using the YuMO (IBR-2) instrument (FLNP, JINR; Dubna, Russian Federation) equipped with a He3-fulfilled, 8 independent wire detector. One solute concentration of 0.40 mg/ml was measured at 20°C. SANS measurements were performed with a two-detector system (sample-detector distances of 4.5 m and 12.97 m). The wavelengths used are from 0.05 to 0.8 nm, the contributions of which are separated using time-of-flight technology.

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 and trimers of dimers at 4000 mM NaCl. Fitting the experimental SANS curve to the theoretical curve for a mixture of the NpSRII/NpHtrII dimers and the "transmembrane-bound" trimers of dimers resulted in χ2 = 5.4. In contrast, fitting the same SANS curve to a theoretical curve based on a mixture of the NpSRII/NpHtrII dimers and the "tripod"-shaped trimers of dimers (Fig. 4B) resulted in χ2 = 1.3, which confirms this "tripod"-shaped model. The volume fractions of dimers and "tripod"-saped trimers of dimers are 63.6% and 36.4%, respectively.

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