9VDM

Cryo-EM structure of human ATP9A (AMPPCP) E2P state open form

9VDM の概要

• エントリーDOI: 10.2210/pdb9vdm/pdb
• EMDBエントリー: 64988
• 分子名称: Probable phospholipid-transporting ATPase IIA, MAGNESIUM ION, O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine, ... (4 entities in total)
• 機能のキーワード: p-type atpase, flippase, human, transport protein
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 116174.81

構造登録者

Abe, K. (登録日: 2025-06-09, 公開日: 2025-09-03, 最終更新日: 2025-10-01)

主引用文献

Abe, K.,Marimuthu, P.,Qian, Y.,Gopalasingam, C.C.,Gerle, C.,Shigematsu, H.,Tanaka, K.,Khandelia, H.
A unique gating mechanism revealed by the cryo-EM structure of monomeric ATP9A flippase.
J.Biol.Chem., 301:110631-110631, 2025

PubMed Abstract: Among mammalian P4-ATPase flippases, only ATP9A and ATP9B do not require the auxiliary subunit CDC50 protein. Whilst its yeast homologue, Neo1, is essential for cell survival, little is known about mammalian ATP9A. We present cryo-EM structures of human monomeric ATP9A at a resolution reaching to 2.2Å, in the outward-facing E2P state. Two distinguishable conformations were obtained from a single sample, one with its outward gate open, and the other in its closed form. Unlike canonical gating observed for most P-type ATPases, which is driven by the movement of transmembrane (TM) helices 1 and 2 linked to the A domain, outward gating in ATP9A is achieved by the movement of TM6-10 helices, likely initiated by the unwinding of TM6. As a result, the volume of the phospholipid binding cavity in the open state surpasses that of other flippases, which could allow binding of phospholipids with larger hydrophilic head groups than that of phosphatidylserine. ATP9A shows an ATPase activity that is significantly increased by the addition of phospholipids that retain the overall negative charge, including phosphatidylserine, phosphatidylinositol and its phosphorylated species, compared to other electroneutral phospholipids. The observation of spontaneous binding of phosphorylated species of phosphatidylinositol in molecular simulation reinforces this fact. Our data provide mechanistic rationales for ATP9A gating, achieved by the rearrangement of the second half of the TM helices. Since TM4 - TM10 is anchored by the CDC50 protein subunit in other flippases, the here observed outward gating mechanism is unique to P4B-type flippases which function as a monomer.

PubMed: 40876594
DOI: 10.1016/j.jbc.2025.110631

実験手法

ELECTRON MICROSCOPY (3.01 Å)