Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods.

Powers KT, Lavering ED, Washington MT, J Mol Biol 430(24):5294-5303 (2018) Europe PMC

SASDED6 – Proliferating cell nuclear antigen - UbPCNA - Split Fusion Trimer

Proliferating cell nuclear antigen
MWexperimental 117 kDa
MWexpected 117 kDa
VPorod 238 nm3
log I(s) 1.59×102 1.59×101 1.59×100 1.59×10-1
Proliferating cell nuclear antigen small angle scattering data  s, nm-1
ln I(s)
Proliferating cell nuclear antigen Guinier plot ln 1.60×102 Rg: 4.1 nm 0 (4.1 nm)-2 s2
(sRg)2I(s)/I(0)
Proliferating cell nuclear antigen Kratky plot 1.104 0 3 sRg
p(r)
Proliferating cell nuclear antigen pair distance distribution function Rg: 4.1 nm 0 Dmax: 14.0 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Proliferating cell nuclear antigen UIOWA_BD model

Synchrotron SAXS data were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the BioCAT 18-ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA). Data were acquired using a reverse-biased silicon diode array Pilatus3 1M detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Poly-histidine tagged ubiquitin-proliferating cell nuclear antigen (UbPCNA) was measured as a split fusion protein (PCNA (1-163, His-Ub-165-258) at a sample injection concentration of 20.70 mg/ml at 22°C using a Wyatt Technology WTC-030S5 (SN 0787), WTC - 015 S5 column with a sample injection volume of 400μL sample at a flow-rate of 0.9 mL/min. The mobile phase was 20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP, pH 7.5. 320 successive 0.500 second SAXS data frames were collected through the SEC-elution profile that underwent appropriate date reduction, background correction (buffer subtraction) scaling and averaging to generate the profile displayed in this entry. The model represents a one state from an ensemble trajectory of ubiquitin-modified PCNA. The full ensemble is included in the full-entry zip archive (ca. 300 MB).

Proliferating cell nuclear antigen (PCNA)
Mol. type   Protein
Organism   Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Olig. state   Trimer
Mon. MW   39.1 kDa
 
UniProt   P15873
Sequence   FASTA