Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin

Yang W, Kim S, Kim M, Shin H, Lee J, Sandmann A, Park O, Dissmeyer N, Song H, Nature Communications 16(1) (2025) DOI

SASDWM2 – Wild-type E3 ubiquitin-protein ligase PRT1 (Proteolysis1)

E3 ubiquitin-protein ligase PRT1
MWI(0) 44 kDa
MWexpected 46 kDa
VPorod 61 nm3
log I(s) 1.64×10-1 1.64×10-2 1.64×10-3 1.64×10-4
E3 ubiquitin-protein ligase PRT1 small angle scattering data  s, nm-1
ln I(s)
E3 ubiquitin-protein ligase PRT1 Guinier plot ln 1.64×10-1 Rg: 3.4 nm 0 (3.4 nm)-2 s2
(sRg)2I(s)/I(0)
E3 ubiquitin-protein ligase PRT1 Kratky plot 1.104 0 √3 sRg
p(r)
E3 ubiquitin-protein ligase PRT1 pair distance distribution function Rg: 3.6 nm 0 Dmax: 12.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
E3 ubiquitin-protein ligase PRT1 DAMMIF model
log I(s)
 s, nm-1
E3 ubiquitin-protein ligase PRT1 ALPHAFOLD PROTEIN STRUCTURE DATABASE model
Synchrotron SAXS data from solutions of PRT1 in 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM TCEP, and 2% (w/v) glycerol were collected on the BL-10C beam line at the Photon Factory (PF), High Energy Accelerator Research Organization (KEK; Tsukuba, Japan) using a Pilatus3 2M detector at a sample-detector distance of 3.0 m and at a wavelength of λ = 0.15 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 250.00 μl sample at 10 mg/ml was injected at different flow rates in the protein peak (20 sec/image with flow at 0.05 ml/min) and the base line (20 sec/image with flow at 0.5 ml/min) using a GE Superdex 200 Increase 10/300 column at 25°C. 332 successive 20-second frames were collected.

E3 ubiquitin-protein ligase PRT1 (PRT1)
Mol. type   Protein
Organism   Arabidopsis thaliana
Olig. state   Monomer
Mon. MW   45.9 kDa
 
UniProt   Q8LBL5 (1-410)
Sequence   FASTA
 
ALPHAFOLD ID   Q8LBL5