+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8sgj | ||||||||||||
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タイトル | Cryo-EM structure of human NCX1 in apo inactivated state | ||||||||||||
要素 |
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キーワード | TRANSPORT PROTEIN (運搬体タンパク質) / Na/Ca exchanger / sodium calcium exchanger | ||||||||||||
機能・相同性 | 機能・相同性情報 relaxation of smooth muscle / vascular associated smooth muscle contraction / calcium ion export / regulation of cell communication by electrical coupling / calcium:sodium antiporter activity / sodium ion export across plasma membrane / membrane depolarization during cardiac muscle cell action potential / regulation of the force of heart contraction / intracellular sodium ion homeostasis / negative regulation of protein serine/threonine kinase activity ...relaxation of smooth muscle / vascular associated smooth muscle contraction / calcium ion export / regulation of cell communication by electrical coupling / calcium:sodium antiporter activity / sodium ion export across plasma membrane / membrane depolarization during cardiac muscle cell action potential / regulation of the force of heart contraction / intracellular sodium ion homeostasis / negative regulation of protein serine/threonine kinase activity / sodium ion import across plasma membrane / calcium ion import / cardiac muscle cell development / calcium ion transport into cytosol / Sodium/Calcium exchangers / regulation of cardiac muscle contraction by calcium ion signaling / calcium ion transmembrane import into cytosol / relaxation of cardiac muscle / cell communication by electrical coupling involved in cardiac conduction / Reduction of cytosolic Ca++ levels / ankyrin binding / negative regulation of cytosolic calcium ion concentration / cellular response to caffeine / positive regulation of the force of heart contraction / calcium ion import across plasma membrane / 介在板 / regulation of cardiac conduction / sodium ion transmembrane transport / calcium ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of bone mineralization / axon terminus / monoatomic ion transport / cardiac muscle contraction / Ion homeostasis / 横行小管 / response to muscle stretch / cytoskeletal protein binding / regulation of heart rate / muscle contraction / cell periphery / calcium ion transmembrane transport / 筋鞘 / cellular response to reactive oxygen species / Z disc / intracellular calcium ion homeostasis / postsynapse / 遺伝子発現の調節 / transmembrane transporter binding / postsynaptic density / calmodulin binding / 神経繊維 / neuronal cell body / シナプス / 樹状突起 / calcium ion binding / 核質 / 細胞膜 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) Mus musculus (ハツカネズミ) | ||||||||||||
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: 3.1 Å | ||||||||||||
データ登録者 | Xue, J. / Jiang, Y. | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Structural mechanisms of the human cardiac sodium-calcium exchanger NCX1. 著者: Jing Xue / Weizhong Zeng / Yan Han / Scott John / Michela Ottolia / Youxing Jiang / 要旨: Na/Ca exchangers (NCX) transport Ca in or out of cells in exchange for Na. They are ubiquitously expressed and play an essential role in maintaining cytosolic Ca homeostasis. Although extensively ...Na/Ca exchangers (NCX) transport Ca in or out of cells in exchange for Na. They are ubiquitously expressed and play an essential role in maintaining cytosolic Ca homeostasis. Although extensively studied, little is known about the global structural arrangement of eukaryotic NCXs and the structural mechanisms underlying their regulation by various cellular cues including cytosolic Na and Ca. Here we present the cryo-EM structures of human cardiac NCX1 in both inactivated and activated states, elucidating key structural elements important for NCX ion exchange function and its modulation by cytosolic Ca and Na. We demonstrate that the interactions between the ion-transporting transmembrane (TM) domain and the cytosolic regulatory domain define the activity of NCX. In the inward-facing state with low cytosolic [Ca], a TM-associated four-stranded β-hub mediates a tight packing between the TM and cytosolic domains, resulting in the formation of a stable inactivation assembly that blocks the TM movement required for ion exchange function. Ca binding to the cytosolic second Ca-binding domain (CBD2) disrupts this inactivation assembly which releases its constraint on the TM domain, yielding an active exchanger. Thus, the current NCX1 structures provide an essential framework for the mechanistic understanding of the ion transport and cellular regulation of NCX family proteins. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8sgj.cif.gz | 195.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8sgj.ent.gz | 145.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8sgj.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sg/8sgj ftp://data.pdbj.org/pub/pdb/validation_reports/sg/8sgj | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 109181.070 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SLC8A1, CNC, NCX1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P32418 |
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-抗体 , 2種, 2分子 LH
#2: 抗体 | 分子量: 21740.082 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) |
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#3: 抗体 | 分子量: 26435.598 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) |
-非ポリマー , 3種, 10分子
#4: 化合物 | ChemComp-CA / #5: 化合物 | #6: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-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 |
-試料調製
構成要素 |
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由来(天然) |
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由来(組換発現) | 生物種: Homo sapiens (ヒト) | ||||||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 60 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19.2_4158: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 133999 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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