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

SASDLE3 – Ubiquitin activating enzyme 5 with ubiquitin-fold modifier 1 (UBA5 9 mg/mL + UFM1 2.25 mg/mL)

Ubiquitin-like modifier-activating enzyme 5
Ubiquitin fold modifer 1
MWexperimental 67 kDa
MWexpected 77 kDa
VPorod 111 nm3
log I(s) 3.01×10-2 3.01×10-3 3.01×10-4 3.01×10-5
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 3.01×10-2 Rg: 3.2 nm 0 (3.2 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: 3.3 nm 0 Dmax: 14.5 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 9 mg/mL + UFM1 2.25 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 (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 9.00 mg/ml was measured at 20°C. 30 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 code   5IAA
 
PDB code   1WXS