7P16

Structure of caspase-3 cleaved rXKR9 in complex with a sybody at 4.3A

Summary for 7P16

• Entry DOI: 10.2210/pdb7p16/pdb
• Related: 7P14
• EMDB information: 13157
• Descriptor: XK-related protein, Sybody, DIUNDECYL PHOSPHATIDYL CHOLINE (3 entities in total)
• Functional Keywords: small membrane protein, in complex with sybody, apoptotic lipid scrambling, membrane protein
• Biological source: Rattus norvegicus (Rat); More
• Total number of polymer chains: 2
• Total formula weight: 57861.19

Authors

Straub, M.S.,Sawicka, M.,Dutzler, R. (deposition date: 2021-07-01, release date: 2021-07-28)

Primary citation

Straub, M.S.,Alvadia, C.,Sawicka, M.,Dutzler, R.
Cryo-EM structures of the caspase activated protein XKR9 involved in apoptotic lipid scrambling.
Elife, 10:-, 2021

PubMed Abstract: The exposure of the negatively charged lipid phosphatidylserine on the cell surface, catalyzed by lipid scramblases, is an important signal for the clearance of apoptotic cells by macrophages. The protein XKR9 is a member of a conserved family that has been associated with apoptotic lipid scrambling. Here, we describe structures of full-length and caspase-treated XKR9 from in complex with a synthetic nanobody determined by cryo-electron microscopy. The 43 kDa monomeric membrane protein can be divided into two structurally related repeats, each containing four membrane-spanning segments and a helix that is partly inserted into the lipid bilayer. In the full-length protein, the C-terminus interacts with a hydrophobic pocket located at the intracellular side acting as an inhibitor of protein function. Cleavage by caspase-3 at a specific site releases 16 residues of the C-terminus, thus making the pocket accessible to the cytoplasm. Collectively, the work has revealed the unknown architecture of the XKR family and has provided initial insight into its activation by caspases.

PubMed: 34263724
DOI: 10.7554/eLife.69800

Experimental method

ELECTRON MICROSCOPY (4.3 Å)