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基本情報
登録情報 | データベース: PDB / ID: 8xej | ||||||||||||
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タイトル | Cryo-EM structure of human XKR8-basigin complex in lipid nanodisc | ||||||||||||
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![]() | LIPID TRANSPORT / scramblase / apoptosis / membrane protein | ||||||||||||
機能・相同性 | ![]() Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / tolerance induction to self antigen / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / phospholipid scramblase activity / neutrophil clearance / dendrite self-avoidance / response to mercury ion ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / phosphatidylserine exposure on apoptotic cell surface / tolerance induction to self antigen / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / phospholipid scramblase activity / neutrophil clearance / dendrite self-avoidance / response to mercury ion / cell-cell adhesion mediator activity / engulfment of apoptotic cell / endothelial tube morphogenesis / neural retina development / Pyruvate metabolism / apoptotic process involved in development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / homophilic cell adhesion via plasma membrane adhesion molecules / D-mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / positive regulation of myoblast differentiation / Integrin cell surface interactions / response to cAMP / embryo implantation / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / neutrophil chemotaxis / establishment of localization in cell / protein localization to plasma membrane / axon guidance / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / virus receptor activity / signaling receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / axon / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / membrane / plasma membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() ![]() | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.66 Å | ||||||||||||
![]() | Sakuragi, T.S. / Kanai, R.K. / Kikkawa, M.K. / Toyoshima, C.T. / Nagata, S.N. | ||||||||||||
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![]() | ![]() タイトル: The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase. 著者: Takaharu Sakuragi / Ryuta Kanai / Mayumi Otani / Masahide Kikkawa / Chikashi Toyoshima / Shigekazu Nagata / ![]() 要旨: XK-related 8 (XKR8), in complex with the transmembrane glycoprotein basigin, functions as a phospholipid scramblase activated by the caspase-mediated cleavage or phosphorylation of its C-terminal ...XK-related 8 (XKR8), in complex with the transmembrane glycoprotein basigin, functions as a phospholipid scramblase activated by the caspase-mediated cleavage or phosphorylation of its C-terminal tail. It carries a putative phospholipid translocation path of multiple hydrophobic and charged residues in the transmembrane region. It also has a crucial tryptophan at the exoplasmic end of the path that regulates its scrambling activity. We herein investigated the tertiary structure of the human XKR8-basigin complex embedded in lipid nanodiscs at an overall resolution of 3.66 Å. We found that the C-terminal tail engaged in intricate polar and van der Waals interactions with a groove at the cytoplasmic surface of XKR8. These interactions maintained the inactive state of XKR8. Point mutations to disrupt these interactions strongly enhanced the scrambling activity of XKR8, suggesting that the activation of XKR8 is mediated by releasing the C-terminal tail from the cytoplasmic groove. We speculate that the cytoplasmic tail region of XKR8 functions as a plug to prevent the scrambling of phospholipids. | ||||||||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 174 KB | 表示 | ![]() |
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PDB形式 | ![]() | 133.8 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 36.5 KB | 表示 | |
CIF形式データ | ![]() | 53.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 38291MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 19592.814 Da / 分子数: 1 / 変異: N152Q, N186Q / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P35613 |
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#2: タンパク質 | 分子量: 45975.609 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q9H6D3 |
#3: 抗体 | 分子量: 22869.639 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#4: 抗体 | 分子量: 23261.865 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#5: 化合物 | ChemComp-DLP / |
研究の焦点であるリガンドがあるか | Y |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 |
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分子量 | 値: 0.11 MDa / 実験値: NO | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7 | ||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1800 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
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解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3次元再構成 | 解像度: 3.66 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 162528 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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