New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.

Thach TT, Shin D, Han S, Lee S, Acta Crystallogr D Struct Biol 72(Pt 4):524-35 (2016) Europe PMC

SASDBQ2 – Human linear tetraubiquitin

Human linear tetra-ubiquitin
MWexperimental 37 kDa
MWexpected 34 kDa
VPorod 49 nm3
log I(s) 1.03×102 1.03×101 1.03×100 1.03×10-1
Human linear tetra-ubiquitin small angle scattering data  s, nm-1
ln I(s)
Human linear tetra-ubiquitin Guinier plot ln 1.03×102 Rg: 3.1 nm 0 (3.1 nm)-2 s2
(sRg)2I(s)/I(0)
Human linear tetra-ubiquitin Kratky plot 1.104 0 3 sRg
p(r)
Human linear tetra-ubiquitin pair distance distribution function Rg: 3.5 nm 0 Dmax: 11.2 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Human linear tetraubiquitin Rg histogram Rg, nm
Human linear tetra-ubiquitin EOM/RANCH model
Human linear tetra-ubiquitin EOM/RANCH model

Synchrotron SAXS data from solutions of Human linear tetraubiquitin in 50 mM Tris 150mM NaCl 0.5 mM EDTA, pH 7.5 were collected on the 5C beam line at the Pohang Accelerator Laboratory storage ring (Pohang, South Korea) using a ADSC Quantum 315 detector at a sample-detector distance of 1.4 m and at a wavelength of λ = 1.907 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 1.8 mg/ml were measured . Five successive 60 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.

Note: The displayed results show a merged data set derived from a concentration series. Data were normalised to protein concentration and the high angle data from highest concentration and low angle data from lowest concentration were merged to generate final SAXS profile. Because of the flexibility of linear-tetraubiquitin molecule, ensemble optimisation method, EOM, was performed. The models shown above are two tetraubiquitin examples from the final EOM output. All EOM models, the radius of gyration distribution and maximum particle dimension distribution can be found in the full entry zip archive.

Human linear tetra-ubiquitin (tetraubiquitin)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   34.2 kDa
 
UniProt   Q5U5U6
Sequence   FASTA