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基本情報
登録情報 | データベース: PDB / ID: 9cgp | ||||||||||||||||||
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タイトル | RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in the absence of calcium with refined P1 domain | ||||||||||||||||||
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![]() | MEMBRANE PROTEIN / Ryanodine receptor / Calcium channel / Mutation / Y523S / RyR1 / dantrolene | ||||||||||||||||||
機能・相同性 | ![]() ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / insulin secretion involved in cellular response to glucose stimulus / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity ...ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / insulin secretion involved in cellular response to glucose stimulus / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / ossification involved in bone maturation / 'de novo' protein folding / negative regulation of heart rate / skin development / FK506 binding / organelle membrane / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / smooth muscle contraction / toxic substance binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / T cell proliferation / smooth endoplasmic reticulum / striated muscle contraction / voltage-gated calcium channel activity / calcium channel inhibitor activity / skeletal muscle fiber development / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / calcium channel complex / sarcoplasmic reticulum membrane / calcium channel regulator activity / muscle contraction / cellular response to calcium ion / protein maturation / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / calcium-mediated signaling / sarcolemma / calcium ion transmembrane transport / calcium channel activity / Stimuli-sensing channels / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / positive regulation of cytosolic calcium ion concentration / protein refolding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / signaling receptor binding / calcium ion binding / ATP binding / identical protein binding / membrane / cytoplasm 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: 3.34 Å | ||||||||||||||||||
![]() | Iyer, K.A. / Samso, M. | ||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Dantrolene inhibition of ryanodine receptor 1 carrying the severe malignant hyperthermia mutation Y522S visualized by cryo-EM. 著者: Kavita A Iyer / Takuya Kobayashi / Takashi Murayama / Montserrat Samsó / ![]() ![]() 要旨: Mutations in the skeletal isoform of the ryanodine receptor 1 (RyR1) pose grave risks during anesthesia or treatment with succinylcholine muscle relaxants. These can trigger a potentially lethal ...Mutations in the skeletal isoform of the ryanodine receptor 1 (RyR1) pose grave risks during anesthesia or treatment with succinylcholine muscle relaxants. These can trigger a potentially lethal malignant hyperthermia (MH) episode via intracellular calcium increase mainly from RyR1 channel leakage. Dantrolene is the only known treatment option to prevent death. The main target of dantrolene is RyR1; however, little is known about the mechanism of inhibition. Cryoelectron microscopy (cryo-EM) structures of dantrolene bound to the severe MH Y522S RyR1 mutant in the closed and open states at 2.5-3.3 Å resolution revealed that the drug binds to the channel's cytoplasmic assembly, far from the ion gate, interacting with residues W882, W996, and R1000 in the P1 domain. The finding was validated by Ca imaging and [H]ryanodine binding in wild-type (WT) and alanine mutants. Dantrolene reduced channel opening probability by restricting the central activation module, "cooling down" the primed conformation caused by the mutation. | ||||||||||||||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 3.2 MB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 1.4 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.6 MB | 表示 | |
XML形式データ | ![]() | 401.2 KB | 表示 | |
CIF形式データ | ![]() | 622.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 45584MC C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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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: 565832.562 Da / 分子数: 4 / 変異: Y523S / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 11667.305 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P68106, peptidylprolyl isomerase #3: 化合物 | ChemComp-ZN / #4: 化合物 | ChemComp-ATP / #5: 化合物 | ChemComp-U1C / 分子量: 314.253 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C14H10N4O5 / タイプ: SUBJECT OF INVESTIGATION 研究の焦点であるリガンドがあるか | Y | Has protein modification | N | |
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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: RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in the absence of calcium with refined P1 domain タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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分子量 | 値: 2.26 MDa / 実験値: NO | |||||||||||||||||||||||||||||||||||
由来(天然) | 生物種: ![]() ![]() | |||||||||||||||||||||||||||||||||||
由来(組換発現) | 生物種: ![]() | |||||||||||||||||||||||||||||||||||
緩衝液 | pH: 7.4 | |||||||||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 277 K |
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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: TFS KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 2600 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 2.69 sec. / 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 4 / 実像数: 13992 |
電子光学装置 | エネルギーフィルタースリット幅: 10 eV |
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解析
EMソフトウェア |
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 1749151 | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.34 Å / 解像度の算出法: OTHER / 粒子像の数: 249034 詳細: The P1 domain (at the corners) was refined using focused alignment and combined with the original 3.34 A-resolution map クラス平均像の数: 3 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 7T64 Accession code: 7T64 / Source name: PDB / タイプ: experimental model |