7BSP

Cryo-EM structure of a human ATP11C-CDC50A flippase in E1-AMPPCP state

Summary for 7BSP

• Entry DOI: 10.2210/pdb7bsp/pdb
• EMDB information: 30163
• Descriptor: ATP11C, CDC50A, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: flippase, p-type atpase, p4-atpase, phospholipid, membrane protein
• Biological source: Homo sapiens; More
• Total number of polymer chains: 2
• Total formula weight: 166676.44

Authors

Abe, K.,Nishizawa, T.,Nakanishi, H. (deposition date: 2020-03-31, release date: 2020-09-30, Last modification date: 2020-10-14)

Primary citation

Nakanishi, H.,Nishizawa, T.,Segawa, K.,Nureki, O.,Fujiyoshi, Y.,Nagata, S.,Abe, K.
Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM.
Cell Rep, 32:108208-108208, 2020

PubMed Abstract: ATP11C, a plasma membrane phospholipid flippase, maintains the asymmetric distribution of phosphatidylserine accumulated in the inner leaflet. Caspase-dependent inactivation of ATP11C is essential for an apoptotic "eat me" signal, phosphatidylserine exposure, which prompts phagocytes to engulf cells. We show six cryo-EM structures of ATP11C at 3.0-4.0 Å resolution in five different states of the transport cycle. A structural comparison reveals phosphorylation-driven domain movements coupled with phospholipid binding. Three structures of phospholipid-bound states visualize phospholipid translocation accompanied by the rearrangement of transmembrane helices and an unwound portion at the occlusion site, and thus they detail the basis for head group recognition and the locality of the protein-bound acyl chains in transmembrane grooves. Invariant Lys880 and the surrounding hydrogen-bond network serve as a pivot point for helix bending and precise P domain inclination, which is crucial for dephosphorylation. The structures detail key features of phospholipid translocation by ATP11C, and a common basic mechanism for flippases is emerging.

PubMed: 32997992
DOI: 10.1016/j.celrep.2020.108208

Experimental method

ELECTRON MICROSCOPY (4 Å)