Cell lysis followed fractionation might cause artifacts that can confound your results.  I would suggest using a non-destructive method such as using a dye to tag your protein and then using high-power microscopy (nanoscopy) to determine its subcellular localization. 

I was using always this one

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2120872/pdf/jc1342529.pdf

a very old, but easy to do (no ultracentrifugation neccessary). May PI always called it "quick and dirty", but it was not that dirty. At least you get a first look on the localizatin of you protein. 

it is similar to what Florian described. 

also when your proteinis may be bound to chromation, use a high salt (300mM or 500mM NaCl) containign buffer to extract it from there. 

lot's of success. 

overexpression causes also artefacts! I guess that was meant by "use a dye to tag your protein"

Thank you Florian, Vicente and Chantal. 

I have thought about trying ChIP-Seq and microscopy, however this particular protein is low in abundance and a good enough antibody isn't available. But yeah, haven't given up these approaches. I just wanted to try out a crude method before getting into those two. Didn't think about using a dye to tag. Thanks!

Thanks for the link, Chantal. I have been trying a similar protocol but this seems more detailed. Thanks!