I want to make structural analysis of lysosomal proteins found in mammals. To make start, I would like to retrieve as many structures as possible from the biological database (PDB). These structures show dynamic structural features (many fold types, variation in size and multiple cellular location). I have tried two general strategies - search by keywork "lysosomal" and get results based on deposition date of structure. I also found an article on proteomic analysis for lysosomal proteins where the author had provided GI for each proteins. In this case, I made protein blast against PDB and selected the lysosomal proteins. Both ways were quite time consuming and again I think my list is still incomplete. Are there any databases for these kind of structures? I would be pleased to get relevant suggestions and help regarding my problem.
You can do this search directly using the advanced search link at the PDB website.
- In the query drop-down, scroll down to "Biology->Cell Component Browser (GO)"
- Enter lysosome: the auto-suggest will provide "lysosome (GO ID:5764)"
- Click "find in tree", then click the link for "lysosome (GO ID:5764)"
Voilà, 330 structures. Add other qualifiers to your search if you wish and submit query to see/retrieve the structures.
What you might want to try is searching [?]UniProt[?] instead. That will allow much more structured search strategies and it has cross-links to [?]PDB[?] for the relevant structures. Now the tricky word in that last sentence is of course "relevant". There definitely are a lot of structures in PDB that are not cross-linked from UniProt, especially many structures for proteins based on (sometimes deliberate) mutations. If you are also looking for those the UniProt approach will not work.
If you Google for "lysosomal proteins database" you will find that there are quite some databases for lysosomal proteins identified in 2D-gel proteomics approaches. I haven't tried these, but it is likely that most of them contain links to UniProt that you could again use to find PDB entries, or maybe even direct PDB links.