Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in Escherichia coli.

Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF, J Biol Chem 295(3):808-821 (2020) Europe PMC

SASDEC9 – Flagellar brake protein YcgR in complex with c-di-GMP from Escherichia coli

Flagellar brake protein YcgR in complex with c-di-GMP
MWexperimental 28 kDa
MWexpected 29 kDa
VPorod 44 nm3
log I(s) 2.75×103 2.75×102 2.75×101 2.75×100
Flagellar brake protein YcgR in complex with c-di-GMP small angle scattering data  s, nm-1
ln I(s)
Flagellar brake protein YcgR in complex with c-di-GMP Guinier plot ln 2.76×103 Rg: 2.2 nm 0 (2.2 nm)-2 s2
(sRg)2I(s)/I(0)
Flagellar brake protein YcgR in complex with c-di-GMP Kratky plot 1.104 0 √3 sRg
p(r)
Flagellar brake protein YcgR in complex with c-di-GMP pair distance distribution function Rg: 2.3 nm 0 Dmax: 7.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Flagellar brake protein YcgR in complex with c-di-GMP PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Flagellar brake protein YcgR in complex with c-di-GMP DAMMIF model
Synchrotron SAXS data from solutions of the flagellar brake protein, YcgR, in bound to cyclic-di-GMP in 20 mM HEPES, 150mM NaCl, 10% glycerol, pH 7.5 were collected on the BL19U2 beam line at the Shanghai Synchrotron Radiation Facility (SSRF; Shanghai, China) using a Pilatus 1M detector at a wavelength of λ = 0.103 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.6 and 4.8 mg/ml were measured at 4°C. 20 successive 1 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 low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

Sample detector distance = UNKNOWN

Flagellar brake protein YcgR in complex with c-di-GMP (YcgR-c-di-GMP)
Mol. type   Protein
Organism   Escherichia coli
Olig. state   Monomer
Mon. MW   29.4 kDa
 
UniProt   P76010
Sequence   FASTA
 
PDB ID   5Y6F