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基本情報
登録情報 | データベース: PDB / ID: 5taz | ||||||
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タイトル | Structure of rabbit RyR1 (ryanodine dataset, class 3) | ||||||
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![]() | TRANSPORT PROTEIN/ISOMERASE / RyR / Ca2+ / EC coupling / gating / TRANSPORT PROTEIN-ISOMERASE complex | ||||||
機能・相同性 | ![]() ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / terminal cisterna / ryanodine receptor complex / negative regulation of release of sequestered calcium ion into cytosol / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation ...ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / terminal cisterna / ryanodine receptor complex / negative regulation of release of sequestered calcium ion into cytosol / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / response to redox state / protein maturation by protein folding / 'de novo' protein folding / skin development / negative regulation of heart rate / organelle membrane / FK506 binding / positive regulation of axon regeneration / cellular response to caffeine / outflow tract morphogenesis / channel regulator activity / intracellularly gated calcium channel activity / smooth muscle contraction / toxic substance binding / smooth endoplasmic reticulum / response to vitamin E / voltage-gated calcium channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / skeletal muscle fiber development / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / T cell proliferation / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium-mediated signaling / response to hydrogen peroxide / calcium channel activity / Stimuli-sensing channels / sarcolemma / 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 / cytosol / 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: 4.3 Å | ||||||
![]() | Clarke, O.B. / des Georges, A. / Zalk, R. / Marks, A.R. / Hendrickson, W.A. / Frank, J. | ||||||
![]() | ![]() タイトル: Structural Basis for Gating and Activation of RyR1. 著者: Amédée des Georges / Oliver B Clarke / Ran Zalk / Qi Yuan / Kendall J Condon / Robert A Grassucci / Wayne A Hendrickson / Andrew R Marks / Joachim Frank / ![]() 要旨: The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple ...The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple functional states revealing the structural basis of channel gating and ligand-dependent activation. Binding sites for the channel activators Ca(2+), ATP, and caffeine were identified at interdomain interfaces of the C-terminal domain. Either ATP or Ca(2+) alone induces conformational changes in the cytoplasmic assembly ("priming"), without pore dilation. In contrast, in the presence of all three activating ligands, high-resolution reconstructions of open and closed states of RyR1 were obtained from the same sample, enabling analyses of conformational changes associated with gating. Gating involves global conformational changes in the cytosolic assembly accompanied by local changes in the transmembrane domain, which include bending of the S6 transmembrane segment and consequent pore dilation, displacement, and deformation of the S4-S5 linker and conformational changes in the pseudo-voltage-sensor domain. | ||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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-関連構造データ
関連構造データ | ![]() 8390MC ![]() 8342C ![]() 8372C ![]() 8373C ![]() 8374C ![]() 8375C ![]() 8376C ![]() 8377C ![]() 8378C ![]() 8379C ![]() 8380C ![]() 8381C ![]() 8382C ![]() 8383C ![]() 8384C ![]() 8385C ![]() 8386C ![]() 8387C ![]() 8388C ![]() 8389C ![]() 8391C ![]() 8392C ![]() 8393C ![]() 8394C ![]() 8395C ![]() 5t15C ![]() 5t9mC ![]() 5t9nC ![]() 5t9rC ![]() 5t9sC ![]() 5t9vC ![]() 5ta3C ![]() 5talC ![]() 5tamC ![]() 5tanC ![]() 5tapC ![]() 5taqC ![]() 5tasC ![]() 5tatC ![]() 5tauC ![]() 5tavC ![]() 5tawC ![]() 5taxC ![]() 5tayC ![]() 5tb0C ![]() 5tb1C ![]() 5tb2C ![]() 5tb3C ![]() 5tb4C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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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: 11798.501 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 475107.719 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #3: 化合物 | ChemComp-ZN / #4: 化合物 | ChemComp-CA / |
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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-Cs2 complex / タイプ: COMPLEX / Entity ID: #1-#2 / 由来: MULTIPLE SOURCES |
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緩衝液 | pH: 7.4 |
試料 | 濃度: 6 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: GOLD / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil |
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: Blotted for 3-4 seconds on both sides with Whatman ashless filter paper, blot force 3, wait time 30 seconds |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 50 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 55564 / アルゴリズム: FOURIER SPACE 詳細: The reported resolution is for the core. The resolution of the whole assembly is 4.6 Angstrom. 対称性のタイプ: POINT |