Structure and dynamics of UBA5-UFM1 complex formation showing new insights in the UBA5 activation mechanism

Fuchs S Kikhney A, Schubert R, Kaiser C, Liebau E, Svergun D, Betzel C, Perbandt M, Journal of Structural Biology :107796 (2021) DOI

SASDLA3 – Ubiquitin activating enzyme 5 with ubiquitin-fold modifier 1 (UBA5 5 mg/mL + UFM1 1.25 mg/ml)

Ubiquitin-like modifier-activating enzyme 5
Ubiquitin fold modifer 1
MWexperimental 60 kDa
MWexpected 77 kDa
VPorod 100 nm3
log I(s) 2.67×10-2 2.67×10-3 2.67×10-4 2.67×10-5
Ubiquitin-like modifier-activating enzyme 5 Ubiquitin fold modifer 1 small angle scattering data  s, nm-1
ln I(s)
Ubiquitin-like modifier-activating enzyme 5 Ubiquitin fold modifer 1 Guinier plot ln 2.68×10-2 Rg: 3.1 nm 0 (3.1 nm)-2 s2
(sRg)2I(s)/I(0)
Ubiquitin-like modifier-activating enzyme 5 Ubiquitin fold modifer 1 Kratky plot 1.104 0 3 sRg
p(r)
Ubiquitin-like modifier-activating enzyme 5 Ubiquitin fold modifer 1 pair distance distribution function Rg: 3.1 nm 0 Dmax: 13 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Ubiquitin-like modifier-activating enzyme 5 Ubiquitin fold modifer 1 SASREF model
Ubiquitin-like modifier-activating enzyme 5 Ubiquitin fold modifer 1 SASREF model
Ubiquitin-like modifier-activating enzyme 5 Ubiquitin fold modifer 1 SASREF model
Ubiquitin-like modifier-activating enzyme 5 Ubiquitin fold modifer 1 PDB (PROTEIN DATA BANK) model

Synchrotron SAXS data from solutions of Ubiquitin activating enzyme 5 with ubiquitin-fold modifier 1 (UBA5 5 mg/mL + UFM1 1.25 mg/ml) in 20 mM Tris, 50 mM NaCl, 2 mM DTT, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123975 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 20°C. 29 successive 0.100 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.

Ubiquitin-like modifier-activating enzyme 5 (UBA5)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   34.2 kDa
 
UniProt   Q9GZZ9 (57-346)
Sequence   FASTA
 
Ubiquitin fold modifer 1 (UFM1)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   8.9 kDa
 
UniProt   P61960 (1-83)
Sequence   FASTA
 
PDB ID   5IAA
 
PDB ID   1WXS