Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.

Miyamoto T, Hayashi Y, Yoshida K, Watanabe H, Uchihashi T, Yonezawa K, Shimizu N, Kamikubo H, Hirota S, ACS Synth Biol (2019) Europe PMC

SASDFS4 – HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))

HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain
MWI(0) 187 kDa
MWexpected 179 kDa
VPorod 642 nm3
log I(s) 4.01×101 4.01×100 4.01×10-1 4.01×10-2
HP0242 from Helicobacter pylori,  N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain small angle scattering data  s, nm-1
ln I(s)
HP0242 from Helicobacter pylori,  N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain Guinier plot ln 4.01×101 Rg: 6.5 nm 0 (6.5 nm)-2 s2
(sRg)2I(s)/I(0)
HP0242 from Helicobacter pylori,  N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain Kratky plot 1.104 0 3 sRg
p(r)
HP0242 from Helicobacter pylori,  N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain pair distance distribution function Rg: 7 nm 0 Dmax: 24 nm

Data validation


Fits and models


log I(s)
 s, nm-1
HP0242 from Helicobacter pylori,  N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain CORAL model

SAXS data from solutions of the fusion protein2 in 20 mM Tris-HCl, 150 mM KCl, pH 8.0 were collected using a Nano-Viewer (Rigaku, Japan) at NAIST (Nara, Japan) equipped with a Pilatus 200K detector at a sample-detector distance of 0.75 m and at a wavelength of λ = 0.15418 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Twenty-five successive 60 second frames were collected at a sample temperature of 20°C. Solute concentrations ranging between 1.9 and 6.8 mg/ml were measured. The data were normalized to the intensity of the direct beam and radially averaged. The scattering from the solvent-blank was subtracted. The scattering profile in this entry represents an extrapolation to infinite dilution.

HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Fusion protein2)
Mol. type   Protein
Organism   Helicobacter pylori, Rattus norvegicus, de novo design
Olig. state   Hexamer
Mon. MW   29.9 kDa
Sequence   FASTA
 
PDB code   3MLI
 
PDB code   1BR0
 
PDB code   4DZL