+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6a69 | ||||||
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タイトル | Cryo-EM structure of a P-type ATPase | ||||||
要素 |
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キーワード | STRUCTURAL PROTEIN (タンパク質) / Membrane protein (膜タンパク質) | ||||||
機能・相同性 | 機能・相同性情報 P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration / regulation of receptor localization to synapse / calcium ion export across plasma membrane / calcium ion transmembrane transporter activity / : / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / regulation of vascular associated smooth muscle contraction / : / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly ...P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration / regulation of receptor localization to synapse / calcium ion export across plasma membrane / calcium ion transmembrane transporter activity / : / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / regulation of vascular associated smooth muscle contraction / : / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / cellular response to corticosterone stimulus / : / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / inhibitory synapse / GABA receptor activation / P-type Ca2+ transporter / neural retina development / P-type calcium transporter activity / cellular response to vitamin D / ATPase-coupled monoatomic cation transmembrane transporter activity / positive regulation of calcium ion transport / dendritic spine membrane / negative regulation of cytokine production / Reduction of cytosolic Ca++ levels / neuronal cell body membrane / positive regulation of protein localization / negative regulation of cytosolic calcium ion concentration / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / Ion transport by P-type ATPases / 免疫シナプス / regulation of cardiac conduction / GABA-ergic synapse / positive regulation of bone mineralization / regulation of cellular response to insulin stimulus / Ion homeostasis / regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / response to cold / cell adhesion molecule binding / long-term synaptic potentiation / positive regulation of long-term synaptic potentiation / PDZ domain binding / 軸索誘導 / brain development / Schaffer collateral - CA1 synapse / visual learning / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / intracellular calcium ion homeostasis / 血圧 / presynaptic membrane / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / positive regulation of protein phosphorylation / 脂質ラフト / apical plasma membrane / 神経繊維 / intracellular membrane-bounded organelle / 樹状突起 / glutamatergic synapse / 細胞膜 / ATP hydrolysis activity / extracellular exosome / 核質 / ATP binding / 生体膜 / metal ion binding / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
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: 4.11 Å | ||||||
データ登録者 | Gong, D.S. / Chi, X.M. / Ren, K. / Huang, G.X.Y. / Zhou, G.W. / Yan, N. / Lei, J.L. / Zhou, Q. | ||||||
引用 | ジャーナル: Nat Commun / 年: 2018 タイトル: Structure of the human plasma membrane Ca-ATPase 1 in complex with its obligatory subunit neuroplastin. 著者: Deshun Gong / Ximin Chi / Kang Ren / Gaoxingyu Huang / Gewei Zhou / Nieng Yan / Jianlin Lei / Qiang Zhou / 要旨: Plasma membrane Ca-ATPases (PMCAs) are key regulators of global Ca homeostasis and local intracellular Ca dynamics. Recently, Neuroplastin (NPTN) and basigin were identified as previously ...Plasma membrane Ca-ATPases (PMCAs) are key regulators of global Ca homeostasis and local intracellular Ca dynamics. Recently, Neuroplastin (NPTN) and basigin were identified as previously unrecognized obligatory subunits of PMCAs that dramatically increase the efficiency of PMCA-mediated Ca clearance. Here, we report the cryo-EM structure of human PMCA1 (hPMCA1) in complex with NPTN at a resolution of 4.1 Å for the overall structure and 3.9 Å for the transmembrane domain. The single transmembrane helix of NPTN interacts with the TM-linker and TM10 of hPMCA1. The subunits are required for the hPMCA1 functional activity. The NPTN-bound hPMCA1 closely resembles the E1-Mg structure of endo(sarco)plasmic reticulum Ca ATPase and the Ca site is exposed through a large open cytoplasmic pathway. This structure provides insight into how the subunits bind to the PMCAs and serves as an important basis for understanding the functional mechanisms of this essential calcium pump family. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6a69.cif.gz | 194.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6a69.ent.gz | 149.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6a69.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/a6/6a69 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/6a69 | 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
#1: タンパク質 | 分子量: 140987.844 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: ATP2B1, PMCA1 / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P20020, EC: 3.6.3.8 |
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#2: タンパク質 | 分子量: 31328.400 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9Y639 |
#3: 糖 | ChemComp-NAG / |
配列の詳細 | THIS SEQUENCE OF NPTN CORRESPOND |
-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 | 名称: complex of one PMCA1 molecular with one NPTN molecular タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 8 |
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 |
-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 |
撮影 | 電子線照射量: 48 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.12_2829: / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.11 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 105188 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
精密化 | 最高解像度: 4.11 Å | ||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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