7DCE

Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment

7DCE の概要

• エントリーDOI: 10.2210/pdb7dce/pdb
• EMDBエントリー: 30636
• 分子名称: Isoform 2 of Basigin, XK-related protein 8, Heavy chain of Fab fragment, ... (5 entities in total)
• 機能のキーワード: xkr8, basigin, scramblase, phospholipid, transport protein
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 112482.01

構造登録者

Sakuragi, T.,Kanai, R.,Tsutsumi, A.,Narita, H.,Onishi, E.,Miyazaki, T.,Baba, T.,Nakagawa, A.,Kikkawa, M.,Toyoshima, C.,Nagata, S. (登録日: 2020-10-26, 公開日: 2021-10-20, 最終更新日: 2024-11-13)

主引用文献

Sakuragi, T.,Kanai, R.,Tsutsumi, A.,Narita, H.,Onishi, E.,Nishino, K.,Miyazaki, T.,Baba, T.,Kosako, H.,Nakagawa, A.,Kikkawa, M.,Toyoshima, C.,Nagata, S.
The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes.
Nat.Struct.Mol.Biol., 28:825-834, 2021

PubMed Abstract: Xkr8-Basigin is a plasma membrane phospholipid scramblase activated by kinases or caspases. We combined cryo-EM and X-ray crystallography to investigate its structure at an overall resolution of 3.8 Å. Its membrane-spanning region carrying 22 charged amino acids adopts a cuboid-like structure stabilized by salt bridges between hydrophilic residues in transmembrane helices. Phosphatidylcholine binding was observed in a hydrophobic cleft on the surface exposed to the outer leaflet of the plasma membrane. Six charged residues placed from top to bottom inside the molecule were essential for scrambling phospholipids in inward and outward directions, apparently providing a pathway for their translocation. A tryptophan residue was present between the head group of phosphatidylcholine and the extracellular end of the path. Its mutation to alanine made the Xkr8-Basigin complex constitutively active, indicating that it plays a vital role in regulating its scramblase activity. The structure of Xkr8-Basigin provides insights into the molecular mechanisms underlying phospholipid scrambling.

PubMed: 34625749
DOI: 10.1038/s41594-021-00665-8

実験手法

ELECTRON MICROSCOPY (3.8 Å)