+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5w3s | |||||||||
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タイトル | Cryo-electron microscopy structure of a TRPML3 ion channel | |||||||||
要素 | Mucolipin-3 isoform 1 | |||||||||
キーワード | TRANSPORT PROTEIN (運搬体タンパク質) / transient receptor potential channel (TRPチャネル) / mucolipin / ion channel (イオンチャネル) / membrane transport / TRPML / TRP channel (TRPチャネル) / calcium channel (カルシウムチャネル) / PIP2 (ホスファチジルイノシトール4,5-ビスリン酸) / PI(3 / 5)P2 / lipid-gated channel / mucolipidosis / lysosomal ion channel / lysosome (リソソーム) | |||||||||
機能・相同性 | 機能・相同性情報 stereocilium membrane / : / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / inner ear auditory receptor cell differentiation / phosphatidylinositol-3,5-bisphosphate binding / monoatomic cation transmembrane transport / autophagosome membrane / locomotory behavior / late endosome membrane / early endosome membrane ...stereocilium membrane / : / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / inner ear auditory receptor cell differentiation / phosphatidylinositol-3,5-bisphosphate binding / monoatomic cation transmembrane transport / autophagosome membrane / locomotory behavior / late endosome membrane / early endosome membrane / protein homotetramerization / membrane => GO:0016020 類似検索 - 分子機能 | |||||||||
生物種 | Callithrix jacchus (コモンマーモセット) | |||||||||
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: 2.94 Å | |||||||||
データ登録者 | Hirschi, M. / Herzik, M.A. / Wie, J. / Suo, Y. / Borschel, W.F. / Ren, D. / Lander, G.C. / Lee, S.Y. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nature / 年: 2017 タイトル: Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3. 著者: Marscha Hirschi / Mark A Herzik / Jinhong Wie / Yang Suo / William F Borschel / Dejian Ren / Gabriel C Lander / Seok-Yong Lee / 要旨: The modulation of ion channel activity by lipids is increasingly recognized as a fundamental component of cellular signalling. The transient receptor potential mucolipin (TRPML) channel family ...The modulation of ion channel activity by lipids is increasingly recognized as a fundamental component of cellular signalling. The transient receptor potential mucolipin (TRPML) channel family belongs to the TRP superfamily and is composed of three members: TRPML1-TRPML3. TRPMLs are the major Ca-permeable channels on late endosomes and lysosomes (LEL). They regulate the release of Ca from organelles, which is important for various physiological processes, including organelle trafficking and fusion. Loss-of-function mutations in the MCOLN1 gene, which encodes TRPML1, cause the neurodegenerative lysosomal storage disorder mucolipidosis type IV, and a gain-of-function mutation (Ala419Pro) in TRPML3 gives rise to the varitint-waddler (Va) mouse phenotype. Notably, TRPML channels are activated by the low-abundance and LEL-enriched signalling lipid phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P), whereas other phosphoinositides such as PtdIns(4,5)P, which is enriched in plasma membranes, inhibit TRPMLs. Conserved basic residues at the N terminus of the channel are important for activation by PtdIns(3,5)P and inhibition by PtdIns(4,5)P. However, owing to a lack of structural information, the mechanism by which TRPML channels recognize PtdIns(3,5)P and increase their Ca conductance remains unclear. Here we present the cryo-electron microscopy (cryo-EM) structure of a full-length TRPML3 channel from the common marmoset (Callithrix jacchus) at an overall resolution of 2.9 Å. Our structure reveals not only the molecular basis of ion conduction but also the unique architecture of TRPMLs, wherein the voltage sensor-like domain is linked to the pore via a cytosolic domain that we term the mucolipin domain. Combined with functional studies, these data suggest that the mucolipin domain is responsible for PtdIns(3,5)P binding and subsequent channel activation, and that it acts as a 'gating pulley' for lipid-dependent TRPML gating. | |||||||||
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 | 5w3s.cif.gz | 649.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5w3s.ent.gz | 543.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5w3s.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/w3/5w3s ftp://data.pdbj.org/pub/pdb/validation_reports/w3/5w3s | 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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-要素
#1: タンパク質 | 分子量: 65092.301 Da / 分子数: 4 / 変異: N138Q / 由来タイプ: 組換発現 由来: (組換発現) Callithrix jacchus (コモンマーモセット) 遺伝子: MCOLN3 / プラスミド: pFastBac / 細胞株 (発現宿主): Sf9 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: F6RG56 #2: 化合物 | ChemComp-Y01 / #3: 化合物 | ChemComp-NA / #4: 化合物 | ChemComp-3PE / #5: 水 | ChemComp-HOH / | |
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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 | 名称: Transient Receptor Potential Mucolipin 3 / タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT |
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分子量 | 値: 0.26 MDa / 実験値: NO |
由来(天然) | 生物種: Callithrix jacchus (コモンマーモセット) |
由来(組換発現) | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) 株: Sf9 / プラスミド: pFastBac |
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 |
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 | 平均露光時間: 12 sec. / 電子線照射量: 63 e/Å2 / 検出モード: SUPER-RESOLUTION 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: 1.11.1_2575: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
対称性 | 点対称性: C4 (4回回転対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.94 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 104084 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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