+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-5776 | |||||||||
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タイトル | Structure of the capsaicin receptor, TRPV1, in complex with DkTx and RTX determined by single particle electron cryo-microscopy | |||||||||
マップデータ | Reconstruction of rat TRPV1 channel in complex with DkTx and RTX | |||||||||
試料 |
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キーワード | TRPV1 channel / DkTx / RTX | |||||||||
機能・相同性 | 機能・相同性情報 temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition ...temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / TRPチャネル / cellular response to acidic pH / thermoception / fever generation / detection of temperature stimulus involved in thermoception / glutamate secretion / dendritic spine membrane / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / response to pH / monoatomic cation transmembrane transporter activity / cellular response to ATP / response to pain / temperature homeostasis / ion channel inhibitor activity / negative regulation of heart rate / cellular response to alkaloid / diet induced thermogenesis / behavioral response to pain / extracellular ligand-gated monoatomic ion channel activity / intracellularly gated calcium channel activity / cellular response to cytokine stimulus / calcium ion import across plasma membrane / negative regulation of mitochondrial membrane potential / detection of temperature stimulus involved in sensory perception of pain / ligand-gated monoatomic ion channel activity / sodium channel regulator activity / potassium channel regulator activity / monoatomic cation channel activity / sensory perception of pain / response to organonitrogen compound / monoatomic ion transmembrane transport / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / calcium ion transmembrane transport / phosphoprotein binding / microglial cell activation / calcium channel activity / lipid metabolic process / response to peptide hormone / cellular response to growth factor stimulus / calcium ion transport / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / cellular response to heat / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / response to heat / toxin activity / postsynaptic membrane / protein homotetramerization / calmodulin binding / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / 樹状突起 / neuronal cell body / negative regulation of transcription by RNA polymerase II / extracellular region / ATP binding / 生体膜 / identical protein binding / metal ion binding / 細胞膜 類似検索 - 分子機能 | |||||||||
生物種 | Rattus norvegicus (ドブネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | |||||||||
データ登録者 | Liao M / Cao E / Julius D / Cheng Y | |||||||||
引用 | ジャーナル: Nature / 年: 2013 タイトル: TRPV1 structures in distinct conformations reveal activation mechanisms. 著者: Erhu Cao / Maofu Liao / Yifan Cheng / David Julius / 要旨: Transient receptor potential (TRP) channels are polymodal signal detectors that respond to a wide range of physical and chemical stimuli. Elucidating how these channels integrate and convert ...Transient receptor potential (TRP) channels are polymodal signal detectors that respond to a wide range of physical and chemical stimuli. Elucidating how these channels integrate and convert physiological signals into channel opening is essential to understanding how they regulate cell excitability under normal and pathophysiological conditions. Here we exploit pharmacological probes (a peptide toxin and small vanilloid agonists) to determine structures of two activated states of the capsaicin receptor, TRPV1. A domain (consisting of transmembrane segments 1-4) that moves during activation of voltage-gated channels remains stationary in TRPV1, highlighting differences in gating mechanisms for these structurally related channel superfamilies. TRPV1 opening is associated with major structural rearrangements in the outer pore, including the pore helix and selectivity filter, as well as pronounced dilation of a hydrophobic constriction at the lower gate, suggesting a dual gating mechanism. Allosteric coupling between upper and lower gates may account for rich physiological modulation exhibited by TRPV1 and other TRP channels. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_5776.map.gz | 45.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-5776-v30.xml emd-5776.xml | 10.1 KB 10.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_5776_1.jpg | 133.3 KB | ||
その他 | TRPV1_DkTx_RTX_sharpened_-150_3.8A.map | 64 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-5776 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5776 | HTTPS FTP |
-関連構造データ
-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_5776.map.gz / 形式: CCP4 / 大きさ: 62.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of rat TRPV1 channel in complex with DkTx and RTX | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.2156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-添付マップデータ: TRPV1 DkTx RTX sharpened -150 3.8A.map
ファイル | TRPV1_DkTx_RTX_sharpened_-150_3.8A.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Rat TRPV1 in complex with DkTx and resiniferatoxin
全体 | 名称: Rat TRPV1 in complex with DkTx and resiniferatoxin |
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要素 |
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-超分子 #1000: Rat TRPV1 in complex with DkTx and resiniferatoxin
超分子 | 名称: Rat TRPV1 in complex with DkTx and resiniferatoxin / タイプ: sample / ID: 1000 / 詳細: The sample was monodisperse / 集合状態: tetramer / Number unique components: 1 |
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分子量 | 実験値: 300 KDa / 理論値: 300 KDa |
-分子 #1: TRPV1
分子 | 名称: TRPV1 / タイプ: protein_or_peptide / ID: 1 詳細: Functional minimal construct containing residues 110-603 and 627-764. コピー数: 1 / 集合状態: Tetramer / 組換発現: Yes |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) / 別称: Rat / 細胞中の位置: Plasma membrane |
分子量 | 実験値: 300 KDa / 理論値: 300 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: HEK293S GnTI / 組換プラスミド: pFastBac1 |
配列 | UniProtKB: TRPV1 |
-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 | 0.3 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP |
グリッド | 詳細: 400 mesh Quantifoil grid |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 120 K / 装置: FEI VITROBOT MARK III / 手法: Blot for 6 sec |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 31000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.5 µm / 倍率(公称値): 31000 |
試料ステージ | 試料ホルダー: Cooled to Liquid Nitrogen temperature / 試料ホルダーモデル: OTHER |
詳細 | Gatan K2 Summit operated in super-resolution counting mode; image recorded with dose fractionation method. |
日付 | 2013年1月1日 |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: GATAN K2 (4k x 4k) / 実像数: 900 / 平均電子線量: 21 e/Å2 詳細: Every image is the average of 30 frames recorded using the K2 Summit. The final reconstruction was calculated from images averaged from frames #3-#16. |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: Each particle |
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最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 3.8 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: RELION / 使用した粒子像数: 36158 |
詳細 | 3D classification, refinement, and reconstruction were performed using RELION. |