Site-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion.

Shin D, Na W, Lee JH, Kim G, Baek J, Park SH, Choi CY, Lee S, Elife 6 (2017) Europe PMC

SASDCM6 – Small GTPase Rab5 conjugated with ubiquitin at K116

Monoubiquitinated Rab5 at K165
MWexperimental 30 kDa
MWexpected 32 kDa
log I(s) 7.30×10-1 7.30×10-2 7.30×10-3 7.30×10-4
Monoubiquitinated Rab5 at K165 small angle scattering data  s, nm-1
ln I(s)
Monoubiquitinated Rab5 at K165 Guinier plot ln 7.30×10-1 Rg: 2.6 nm 0 (2.6 nm)-2 s2
(sRg)2I(s)/I(0)
Monoubiquitinated Rab5 at K165 Kratky plot 1.104 0 √3 sRg
p(r)
Monoubiquitinated Rab5 at K165 pair distance distribution function Rg: 2.7 nm 0 Dmax: 8.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Small GTPase Rab5 conjugated with ubiquitin at K116 Rg histogram Rg, nm
Monoubiquitinated Rab5 at K165 EOM/RANCH model
Monoubiquitinated Rab5 at K165 EOM/RANCH model
log I(s)
 s, nm-1
Monoubiquitinated Rab5 at K165 DAMMIF model
Synchrotron SAXS data from solutions of Small GTPase Rab5 conjugated with ubiquitin at K116 in 50 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2, pH 7.5 were collected on the 4C beam line at the Pohang Accelerator Laboratory storage ring (Pohang, South Korea) using a ADSC Quantum 315 detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.4 and 2.9 mg/ml were measured at 4°C. Six successive 10 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.

Monoubiquitinated Rab5 at K165 (mUbRab5K165)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   32.2 kDa
Sequence   FASTA