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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 8tkg | ||||||||||||
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タイトル | Human Type 3 IP3 Receptor - Resting State (+IP3/ATP) | ||||||||||||
![]() | Inositol 1,4,5-trisphosphate receptor type 3 | ||||||||||||
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機能・相同性 | ![]() sensory perception of bitter taste / DAG and IP3 signaling / sensory perception of umami taste / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-gated calcium channel activity / sensory perception of sweet taste / platelet dense tubular network membrane / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / PLC beta mediated events ...sensory perception of bitter taste / DAG and IP3 signaling / sensory perception of umami taste / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-gated calcium channel activity / sensory perception of sweet taste / platelet dense tubular network membrane / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / PLC beta mediated events / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() | ||||||||||||
手法 | ![]() ![]() ![]() | ||||||||||||
![]() | Paknejad, N. / Sapuru, V. / Hite, R.K. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural titration reveals Ca-dependent conformational landscape of the IP receptor. 著者: Navid Paknejad / Vinay Sapuru / Richard K Hite / ![]() 要旨: Inositol 1,4,5-trisphosphate receptors (IPRs) are endoplasmic reticulum Ca channels whose biphasic dependence on cytosolic Ca gives rise to Ca oscillations that regulate fertilization, cell division ...Inositol 1,4,5-trisphosphate receptors (IPRs) are endoplasmic reticulum Ca channels whose biphasic dependence on cytosolic Ca gives rise to Ca oscillations that regulate fertilization, cell division and cell death. Despite the critical roles of IPR-mediated Ca responses, the structural underpinnings of the biphasic Ca dependence that underlies Ca oscillations are incompletely understood. Here, we collect cryo-EM images of an IPR with Ca concentrations spanning five orders of magnitude. Unbiased image analysis reveals that Ca binding does not explicitly induce conformational changes but rather biases a complex conformational landscape consisting of resting, preactivated, activated, and inhibited states. Using particle counts as a proxy for relative conformational free energy, we demonstrate that Ca binding at a high-affinity site allows IPRs to activate by escaping a low-energy resting state through an ensemble of preactivated states. At high Ca concentrations, IPRs preferentially enter an inhibited state stabilized by a second, low-affinity Ca binding site. Together, these studies provide a mechanistic basis for the biphasic Ca-dependence of IPR channel activity. | ||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 3.6 MB | 表示 | ![]() |
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PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 41350MC ![]() 8tk8C ![]() 8tkdC ![]() 8tkeC ![]() 8tkfC ![]() 8tkhC ![]() 8tkiC ![]() 8tl9C ![]() 8tlaC 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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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
-タンパク質 , 1種, 4分子 ABCD
#1: タンパク質 | 分子量: 304488.688 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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-非ポリマー , 6種, 684分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/I3P.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/I3P.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/HOH.gif)
#2: 化合物 | ChemComp-ZN / #3: 化合物 | ChemComp-I3P / ![]() #4: 化合物 | ChemComp-CA / #5: 化合物 | ChemComp-ATP / ![]() #6: 化合物 | ChemComp-PCW / #7: 水 | ChemComp-HOH / | ![]() |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: ![]() |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: ![]() |
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試料調製
構成要素 | 名称: Human Type 3 IP3 Receptor / タイプ: COMPLEX 詳細: In the presence of saturating IP3, ATP, and Ca2+ titrated from 1 nM to 10 um Entity ID: #1 / 由来: RECOMBINANT |
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分子量 | 値: 1.2 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: 8 詳細: 120 mM NaCl, 50 mM Tris-HCl pH 8.0, 0.02% LMNG, 2 mM dithiothreitol, 2 mM EDTA, 2 mM EGTA, 2 mM BAPTA, 2 mM HEDTA, 1 mM ATP, 500 uM fluorinated fos-choline-8, 3 mM free Mg2+, 1-10000 nM free Ca2+ |
試料 | 濃度: 20 mg/ml / 包埋: NO / シャドウイング: NO / 染色![]() ![]() |
急速凍結![]() | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 90 % / 凍結前の試料温度: 277 K 詳細: Custom-made calcium free blotting paper (see publication for details). |
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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![]() ![]() |
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: 3 sec. / 電子線照射量: 66 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: 6 / 実像数: 17733 詳細: Images were collected at 0.826 A/px magnification on an FEI Krios with Gatan K3 detector at 15 e-/pix/sec with 3 sec exposure (0.05 sec/frame) for a total dose of 66 e-/A2 in automated ...詳細: Images were collected at 0.826 A/px magnification on an FEI Krios with Gatan K3 detector at 15 e-/pix/sec with 3 sec exposure (0.05 sec/frame) for a total dose of 66 e-/A2 in automated fashion using SerialEM. Five datasets were collected during the same session for each Ca2+ concentration on a series of grids that were prepared sequentially resulting in 637 movies at 1 nM, 2150 movies at 10 nM, 6126 movies at 100 nM, 1372 movies at 1 uM, and 3136 movies at 10 uM. A sixth dataset of 4312 movies collected at nominal 100 nM free Ca2+ from a grid prepared later in the sequence was collected as a technical replicate to assess experimental error. |
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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: 2.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 3668312 / 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 / Target criteria: Map to Model FSC | ||||||||||||||||
精密化 | 交差検証法: NONE |