+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6mu1 | |||||||||||||||||||||
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タイトル | Structure of full-length IP3R1 channel bound with Adenophostin A | |||||||||||||||||||||
要素 | Inositol 1,4,5-trisphosphate receptor type 1 | |||||||||||||||||||||
キーワード | MEMBRANE PROTEIN / inositol 1 / 4 / 5-trisphosphate receptor / calcium release channel / neuronal type 1 / adenophostin A / IP3R-channel activator | |||||||||||||||||||||
機能・相同性 | 機能・相同性情報 Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / calcineurin complex / platelet dense granule membrane ...Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / inositol 1,4,5-trisphosphate-gated calcium channel activity / calcium import into the mitochondrion / regulation of postsynaptic cytosolic calcium ion concentration / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / negative regulation of calcium-mediated signaling / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / endoplasmic reticulum calcium ion homeostasis / positive regulation of hepatocyte proliferation / nuclear inner membrane / transport vesicle membrane / Ion homeostasis / dendrite development / intracellularly gated calcium channel activity / ligand-gated ion channel signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / single fertilization / GABA-ergic synapse / calcium channel inhibitor activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / liver regeneration / phosphatidylinositol binding / secretory granule membrane / post-embryonic development / sarcoplasmic reticulum / synaptic membrane / calcium ion transmembrane transport / calcium-mediated signaling / cell morphogenesis / positive regulation of insulin secretion / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / nuclear envelope / calcium ion transport / presynapse / cellular response to hypoxia / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / protein phosphatase binding / protein homotetramerization / transmembrane transporter binding / postsynapse / postsynaptic density / response to hypoxia / protein domain specific binding / positive regulation of apoptotic process / neuronal cell body / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm 類似検索 - 分子機能 | |||||||||||||||||||||
生物種 | Rattus norvegicus (ドブネズミ) | |||||||||||||||||||||
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: 4.1 Å | |||||||||||||||||||||
データ登録者 | Serysheva, I.I. / Fan, G. / Baker, M.R. / Wang, Z. / Seryshev, A. / Ludtke, S.J. / Baker, M.L. | |||||||||||||||||||||
資金援助 | 米国, 6件
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引用 | ジャーナル: Cell Res / 年: 2018 タイトル: Cryo-EM reveals ligand induced allostery underlying InsPR channel gating. 著者: Guizhen Fan / Mariah R Baker / Zhao Wang / Alexander B Seryshev / Steven J Ludtke / Matthew L Baker / Irina I Serysheva / 要旨: Inositol-1,4,5-trisphosphate receptors (InsPRs) are cation channels that mobilize Ca from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsPR activation is the ...Inositol-1,4,5-trisphosphate receptors (InsPRs) are cation channels that mobilize Ca from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsPR activation is the coupled interplay between binding of InsP and Ca that switches the ion conduction pathway between closed and open states to enable the passage of Ca through the channel. However, the molecular mechanism of how the receptor senses and decodes ligand-binding signals into gating motion remains unknown. Here, we present the electron cryo-microscopy structure of InsPR1 from rat cerebellum determined to 4.1 Å resolution in the presence of activating concentrations of Ca and adenophostin A (AdA), a structural mimetic of InsP and the most potent known agonist of the channel. Comparison with the 3.9 Å-resolution structure of InsPR1 in the Apo-state, also reported herein, reveals the binding arrangement of AdA in the tetrameric channel assembly and striking ligand-induced conformational rearrangements within cytoplasmic domains coupled to the dilation of a hydrophobic constriction at the gate. Together, our results provide critical insights into the mechanistic principles by which ligand-binding allosterically gates InsPR channel. | |||||||||||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6mu1.cif.gz | 1.3 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6mu1.ent.gz | 975 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6mu1.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6mu1_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6mu1_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 6mu1_validation.xml.gz | 281.3 KB | 表示 | |
CIF形式データ | 6mu1_validation.cif.gz | 414.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/mu/6mu1 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/6mu1 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 312442.000 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Rattus norvegicus (ドブネズミ) / 参照: UniProt: P29994 #2: 化合物 | ChemComp-JYP / |
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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 |
-試料調製
構成要素 | 名称: Inositol 1,4,5-trisphosphate receptor / タイプ: COMPLEX / 詳細: tetrameric assembly / Entity ID: #1 / 由来: NATURAL |
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分子量 | 値: 1.3 MDa / 実験値: NO |
由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) / 細胞内の位置: membrane / 器官: Brain / Organelle: endoplasmic reticulum / 組織: Cerebellum |
緩衝液 | pH: 7.4 詳細: 50 mM Tris-HCl buffer (pH 7.4), 150 mM NaCl, 1 mM DTT, 0.4% CHAPS,100 nM of AdA, 300 nM of Ca2+, protease inhibitors |
試料 | 濃度: 0.1 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: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R2/1 |
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: 293 K |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F30 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / Cs: 2 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER 最高温度: 93 K / 最低温度: 93 K |
撮影 | 平均露光時間: 0.2 sec. / 電子線照射量: 1.3 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) 実像数: 14686 |
画像スキャン | 動画フレーム数/画像: 35 / 利用したフレーム数/画像: 2-17 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 191646 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C4 (4回回転対称) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 179760 詳細: Image processing was performed independently using RELION and EMAN2 to near-atomic resolution in large regions of the structure. Local resolution assessment performed independently for each ...詳細: Image processing was performed independently using RELION and EMAN2 to near-atomic resolution in large regions of the structure. Local resolution assessment performed independently for each map revealed different domains were better resolved by each software package. To avoid human bias and extract the most information from each reconstruction the final map was a locally filtered average of the EMAN2 and RELION map. To combine the two maps, a local resolution filter, based on a windowed FSC local resolution assessment, was performed independently on the two maps. The two locally filtered maps were then averaged together. The local filtration determines the contribution of each map at each resolution in each region of the final composite map, permitting each map to dominate in regions where better self-consistency was obtained during refinement. 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL |