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基本情報
登録情報 | データベース: PDB / ID: 5j8v | |||||||||||||||
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タイトル | Structure of rabbit ryanodine receptor RyR1 open state activated by calcium ion | |||||||||||||||
![]() | Ryanodine receptor 1 | |||||||||||||||
![]() | TRANSPORT PROTEIN / endoplasmic reticula / skeletal muscles / intracellular calcium ion channel / activated by calcium ion | |||||||||||||||
機能・相同性 | ![]() ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / 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: 4.9 Å | |||||||||||||||
![]() | Wang, X. / Wei, R. / Yin, C. / Sun, F. | |||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural insights into Ca(2+)-activated long-range allosteric channel gating of RyR1. 著者: Risheng Wei / Xue Wang / Yan Zhang / Saptarshi Mukherjee / Lei Zhang / Qiang Chen / Xinrui Huang / Shan Jing / Congcong Liu / Shuang Li / Guangyu Wang / Yaofang Xu / Sujie Zhu / Alan J ...著者: Risheng Wei / Xue Wang / Yan Zhang / Saptarshi Mukherjee / Lei Zhang / Qiang Chen / Xinrui Huang / Shan Jing / Congcong Liu / Shuang Li / Guangyu Wang / Yaofang Xu / Sujie Zhu / Alan J Williams / Fei Sun / Chang-Cheng Yin / ![]() ![]() 要旨: Ryanodine receptors (RyRs) are a class of giant ion channels with molecular mass over 2.2 mega-Daltons. These channels mediate calcium signaling in a variety of cells. Since more than 80% of the RyR ...Ryanodine receptors (RyRs) are a class of giant ion channels with molecular mass over 2.2 mega-Daltons. These channels mediate calcium signaling in a variety of cells. Since more than 80% of the RyR protein is folded into the cytoplasmic assembly and the remaining residues form the transmembrane domain, it has been hypothesized that the activation and regulation of RyR channels occur through an as yet uncharacterized long-range allosteric mechanism. Here we report the characterization of a Ca(2+)-activated open-state RyR1 structure by cryo-electron microscopy. The structure has an overall resolution of 4.9 Å and a resolution of 4.2 Å for the core region. In comparison with the previously determined apo/closed-state structure, we observed long-range allosteric gating of the channel upon Ca(2+) activation. In-depth structural analyses elucidated a novel channel-gating mechanism and a novel ion selectivity mechanism of RyR1. Our work not only provides structural insights into the molecular mechanisms of channel gating and regulation of RyRs, but also sheds light on structural basis for channel-gating and ion selectivity mechanisms for the six-transmembrane-helix cation channel family. | |||||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 2 MB | 表示 | ![]() |
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PDB形式 | ![]() | 1.4 MB | 表示 | ![]() |
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-関連構造データ
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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: 565908.625 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
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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 |
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試料調製
構成要素 | 名称: rabbit ryanodine receptor RyR1 / タイプ: COMPLEX / Entity ID: all / 由来: NATURAL | |||||||||||||||||||||||||
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分子量 | 値: 2.2 MDa / 実験値: NO | |||||||||||||||||||||||||
由来(天然) | 生物種: ![]() ![]() | |||||||||||||||||||||||||
緩衝液 | pH: 7.4 詳細: 1:1000 diluted protease inhibitor cocktail was also added in buffer | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 5 mg/ml / 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: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R2/2 | |||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K / 詳細: Grids were blotted for 2s before plunging. |
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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 / 倍率(公称値): 59000 X / 倍率(補正後): 100286 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 1000 nm / Calibrated defocus min: 1300 nm / 最大 デフォーカス(補正後): 5400 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER 最高温度: 80 K / 最低温度: 80 K / Residual tilt: 23 mradians |
撮影 | 平均露光時間: 2 sec. / 電子線照射量: 48 e/Å2 / 検出モード: INTEGRATING フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 撮影したグリッド数: 4 / 実像数: 4931 |
画像スキャン | サンプリングサイズ: 14 µm / 横: 4096 / 縦: 4096 / 動画フレーム数/画像: 31 / 利用したフレーム数/画像: 2-31 |
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解析
EMソフトウェア |
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画像処理 | 詳細: The 31 frames of each video were processed into 10 images by merging 3 adjacent frames and then subjected into motion correction using program dosefgpu_driftcorr. | ||||||||||||||||||||||||||||||||
CTF補正 | タイプ: NONE | ||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 376537 | ||||||||||||||||||||||||||||||||
対称性 | 点対称性: C4 (4回回転対称) | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 41743 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL / 空間: RECIPROCAL | ||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 3J8H PDB chain-ID: A / Pdb chain residue range: 1-5037 |