Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.

Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J, Structure 25(3):434-445 (2017) Europe PMC

SASDBV9 – Immunoglobulin domain 4 of Nucleoporin Pom152 (Pom152 Ig-4: amino acids 718-820)

Nucleoporin POM152
MWI(0) 12 kDa
MWexpected 12 kDa
VPorod 18 nm3
log I(s) 1.54×102 1.54×101 1.54×100 1.54×10-1
Nucleoporin POM152 small angle scattering data  s, nm-1
ln I(s)
Nucleoporin POM152 Guinier plot ln 1.54×102 Rg: 1.8 nm 0 (1.8 nm)-2 s2
(sRg)2I(s)/I(0)
Nucleoporin POM152 Kratky plot 1.104 0 √3 sRg
p(r)
Nucleoporin POM152 pair distance distribution function Rg: 1.8 nm 0 Dmax: 6.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Nucleoporin POM152 MODELLER model
log I(s)
 s, nm-1
Nucleoporin POM152 DAMMIN model
Synchrotron SAXS data from solutions of Immunoglobulin domain 4 of Nucleoporin Pom152 (Pom152 Ig-4: amino acids 718-820) in 10mM HEPES, 150mM NaCl, 10%(v/v) glycerol, 5mM DTT, pH 7.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL) (Stanford, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.098 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 11.9 mg/ml were measured at 15°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 and the different curves were scaled for protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

Guinier Rg and I(0) were calculated using AutoRg. The experimental MW was estimated using SAXSMOW.

Nucleoporin POM152
Mol. type   Protein
Organism   Saccharomyces cerevisiae
Olig. state   Monomer
Mon. MW   12.4 kDa
 
UniProt   P39685
Sequence   FASTA
 
PDB ID   5TVZ