+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2807 | |||||||||
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タイトル | Single-particle electron cryo-microscopy structure of ryanodine receptor RyR1 in complex with FKBP12 | |||||||||
マップデータ | Reconstruction of RyR1 | |||||||||
試料 |
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キーワード | ryanodine receptors / intracellular Ca2+ channel / in complex with its modulator FKBP12 / excitation-contraction coupling. | |||||||||
機能・相同性 | 機能・相同性情報 cytoplasmic side of membrane / 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 / cellular response to caffeine / intracellularly gated calcium channel activity ...cytoplasmic side of membrane / 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 / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / cellular response to calcium ion / 筋小胞体 / muscle contraction / プロリルイソメラーゼ / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / intracellular membrane-bounded organelle / calcium ion binding / ATP binding / 生体膜 / identical protein binding / 細胞質基質 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | |||||||||
データ登録者 | Yan Z / Bai XC / Yan CY / Wu JP / Scheres S / Shi YG / Yan N | |||||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution. 著者: Zhen Yan / Xiaochen Bai / Chuangye Yan / Jianping Wu / Zhangqiang Li / Tian Xie / Wei Peng / Changcheng Yin / Xueming Li / Sjors H W Scheres / Yigong Shi / Nieng Yan / 要旨: The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest ...The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5,000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryomicroscopy. Three previously uncharacterized domains, named central, handle and helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative-charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity-filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_2807.map.gz | 166.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2807-v30.xml emd-2807.xml | 10 KB 10 KB | 表示 表示 | EMDBヘッダ |
画像 | RyR1.jpg | 103.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2807 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2807 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_2807.map.gz / 形式: CCP4 / 大きさ: 173.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of RyR1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : rabbit RyR1 in complex with its modulator FKBP12
全体 | 名称: rabbit RyR1 in complex with its modulator FKBP12 |
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要素 |
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-超分子 #1000: rabbit RyR1 in complex with its modulator FKBP12
超分子 | 名称: rabbit RyR1 in complex with its modulator FKBP12 / タイプ: sample / ID: 1000 / 詳細: The sample was monodisperse / 集合状態: 4 / Number unique components: 1 |
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分子量 | 実験値: 5.5 MDa / 理論値: 5.5 MDa / 手法: sequence |
-分子 #1: ryanodine receptor RyR1
分子 | 名称: ryanodine receptor RyR1 / タイプ: protein_or_peptide / ID: 1 / 詳細: The RyR1 is in complex with its modulator FKBP12 / コピー数: 4 / 集合状態: tetramer / 組換発現: No |
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由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) / 別称: Rabbit |
分子量 | 理論値: 5.5 MDa |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 1.6 mg/mL |
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緩衝液 | pH: 8 / 詳細: 25 mM Tris-HCl, 150 mM NaCl, 2 mM DTT |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK III 手法: Aliquots of 3uL of purified RYR1 at a concentration of approximately 30 nM were placed on glow-discharged holey carbon grids (Quantifoil CuR2/2), on which a home-made continuous carbon film ...手法: Aliquots of 3uL of purified RYR1 at a concentration of approximately 30 nM were placed on glow-discharged holey carbon grids (Quantifoil CuR2/2), on which a home-made continuous carbon film had previously been deposited. Grids were blotted for 2 s and flash frozen in liquid ethane using an FEI Vitrobot. |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 104748 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / 最大 デフォーカス(公称値): 5.6 µm / 最小 デフォーカス(公称値): 1.9 µm / 倍率(公称値): 78000 |
試料ステージ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
温度 | 最低: 80 K / 最高: 90 K / 平均: 85 K |
日付 | 2014年6月21日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) デジタル化 - サンプリング間隔: 14 µm / 実像数: 1500 / 平均電子線量: 40 e/Å2 詳細: An in-house built system was used to intercept the videos from the detector at a rate of 17 frames for the 1 s exposures. |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: Each particle |
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最終 再構成 | 想定した対称性 - 点群: C4 (4回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.8 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: CTFFIND3, RELION 詳細: Use a newly developed statistical movie processing approach to compensate for beam-induced movement. 使用した粒子像数: 65872 |
詳細 | The 20 frames of each video were aligned using the whole-image motion correction method. We used the particles picking tool in the RELION for automated selection of particles. |