Human multi-pass integral membrane protein crystal structures

From: Raji Edayathumangalam
Date: 3 March 2012 23:13


Dear fellow CCP4bb-ers,

Does anyone know how many crystal structures have been published to date for unique human multi-pass alpha-helical integral membrane proteins? For example, if there are multiple structures of the same membrane proteins with different ligands, I do not wish to count them as unique for my purposes.

I have already tried to search for this information on Stephen White's database, on Caffrey's page, in the PDB database, Google etc. but my searches either return no results or incomplete results. I am looking for a specific subset of membrane proteins that satisfy all following criteria: "human + multi-pass + alpha-helical + integral membrane protein."

If anyone can provide the answer, that would be very helpful. I need this information for a fellowship application.

Thanks much.

Raji

--
Raji Edayathumangalam

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From: Sean Seaver


Hi Raji,

Here is an approach that I hope helps:

Used the following pages:

http://opm.phar.umich.edu/superfamilies.php?class=1
http://opm.phar.umich.edu/superfamilies.php?class=16

Export/sort by species the second table using your favorite spreadsheet program:
-writing a script for this step maybe helpful

Generates the following list of 96 PDB entries for humans:
http://bit.ly/widcnV (link to Google docs page)

I took a look at each entry and added a short note which is worth double checking.

If you do not want to include structures solved by NMR or entries that differ by additional domains then editing will be needed.  Some entries listed as alpha helical do contain varying amounts of beta sheets which may or may not work for your purposes.

Maybe worth cross referencing with the following database:
http://pdbtm.enzim.hu/?m=sform
(search by alpha helical, transmembrane segments set to 2+ then find all results containing the term human)
note: this output includes theoretical models from PDB, which I suspect you may want to remove

Hopefully, someone will follow up with a more elegant solution and all the best with your application.

Take Care,

Sean Seaver

P212121
http://store.p212121.com/