+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-42769 | |||||||||
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タイトル | Structure of PKA phosphorylated human RyR2-R420W in the open state in the presence of calcium and calmodulin | |||||||||
マップデータ | Composite map of the Structure of PKA phosphorylated human RyR2-R420W in the open state in the presence of calcium and calmodulin | |||||||||
試料 |
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キーワード | calcium channel / MEMBRANE PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 junctional sarcoplasmic reticulum membrane / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / regulation of AV node cell action potential / calcium-induced calcium release activity ...junctional sarcoplasmic reticulum membrane / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / regulation of AV node cell action potential / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / cell communication by electrical coupling involved in cardiac conduction / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / embryonic heart tube morphogenesis / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cardiac muscle hypertrophy / negative regulation of release of sequestered calcium ion into cytosol / ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by calcium ion signaling / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / CaM pathway / Cam-PDE 1 activation / response to muscle activity / calcium ion transport into cytosol / Sodium/Calcium exchangers / response to caffeine / Calmodulin induced events / response to redox state / protein maturation by protein folding / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / 'de novo' protein folding / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of heart rate / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / positive regulation of heart rate / FK506 binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of axon regeneration / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / cellular response to caffeine / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein kinase A regulatory subunit binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / channel regulator activity / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / RHO GTPases activate PAKs / positive regulation of the force of heart contraction / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / smooth muscle contraction / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / smooth endoplasmic reticulum / response to vitamin E / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / eNOS activation / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / T cell proliferation / cardiac muscle contraction / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.56 Å | |||||||||
データ登録者 | Miotto MC / Marks AR | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: To Be Published タイトル: Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders 著者: Miotto MC | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_42769.map.gz | 245.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-42769-v30.xml emd-42769.xml | 23.9 KB 23.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_42769.png | 206.9 KB | ||
Filedesc metadata | emd-42769.cif.gz | 9.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-42769 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42769 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_42769_validation.pdf.gz | 513.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_42769_full_validation.pdf.gz | 513.3 KB | 表示 | |
XML形式データ | emd_42769_validation.xml.gz | 8.1 KB | 表示 | |
CIF形式データ | emd_42769_validation.cif.gz | 9.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42769 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42769 | HTTPS FTP |
-関連構造データ
関連構造データ | 8uxmMC 8uq2C 8uq3C 8uq4C 8uq5C 8uxcC 8uxeC 8uxfC 8uxgC 8uxhC 8uxiC 8uxlC 42751 42752 42753 42754 42755 42756 42757 42758 M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_42769.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Composite map of the Structure of PKA phosphorylated human RyR2-R420W in the open state in the presence of calcium and calmodulin | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.8425 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-試料の構成要素
+全体 : Complex of RyR2-R420W, Calstabin-2, and Calmodulin
+超分子 #1: Complex of RyR2-R420W, Calstabin-2, and Calmodulin
+超分子 #2: Ryanodine Receptor 2
+超分子 #3: Peptidyl- cis-trans isomerase FKBP1B
+超分子 #4: Calmodulin
+分子 #1: Calmodulin-1
+分子 #2: Ryanodine receptor 2
+分子 #3: Peptidyl-prolyl cis-trans isomerase FKBP1B
+分子 #4: CALCIUM ION
+分子 #5: ZINC ION
+分子 #6: ADENOSINE-5'-TRIPHOSPHATE
-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 | 2.5 mg/mL | |||||||||||||||||||||||||||
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緩衝液 | pH: 7.4 構成要素:
詳細: 0.020 mM Calmodulin was added to the final sample | |||||||||||||||||||||||||||
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 80.0 K / 最高: 100.0 K |
特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) デジタル化 - サイズ - 横: 5760 pixel / デジタル化 - サイズ - 縦: 4092 pixel / 平均電子線量: 58.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.2 µm / 最小 デフォーカス(公称値): 0.5 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: INSILICO MODEL / In silico モデル: CryoSPARC ab initio |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.56 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC / 使用した粒子像数: 49606 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |