+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-5777 | |||||||||
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タイトル | Reconstruction of rat TRPV1 channel in complex with capsaicin by single particle cryo-microscopy | |||||||||
マップデータ | Reconstruction of rat TRPV1 in complex with capsaicin | |||||||||
試料 |
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キーワード | TRPV1 channel / capsaicin | |||||||||
機能・相同性 | 機能・相同性情報 temperature-gated ion channel activity / response to capsazepine / 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 / smooth muscle contraction involved in micturition / TRP channels / cellular response to temperature stimulus ...temperature-gated ion channel activity / response to capsazepine / 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 / smooth muscle contraction involved in micturition / TRP channels / cellular response to temperature stimulus / cellular response to acidic pH / excitatory extracellular ligand-gated monoatomic ion channel activity / fever generation / thermoception / detection of temperature stimulus involved in thermoception / glutamate secretion / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / dendritic spine membrane / response to pH / monoatomic cation transmembrane transporter activity / cellular response to ATP / negative regulation of heart rate / temperature homeostasis / response to pain / cellular response to alkaloid / calcium ion import across plasma membrane / diet induced thermogenesis / behavioral response to pain / intracellularly gated calcium channel activity / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / ligand-gated monoatomic ion channel activity / extracellular ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / monoatomic ion transmembrane transport / sensory perception of pain / : / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / lipid metabolic process / phosphoprotein binding / calcium ion transmembrane transport / microglial cell activation / calcium channel activity / transmembrane signaling receptor activity / cellular response to growth factor stimulus / response to peptide hormone / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / cellular response to heat / response to heat / postsynaptic membrane / protein homotetramerization / calmodulin binding / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / dendrite / negative regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane 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: 4.2 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_5777.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-5777-v30.xml emd-5777.xml | 10 KB 10 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_5777_1.jpg | 141.8 KB | ||
その他 | emd_5777_additional_1.map.gz | 59.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-5777 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5777 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_5777_validation.pdf.gz | 360.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_5777_full_validation.pdf.gz | 360.3 KB | 表示 | |
XML形式データ | emd_5777_validation.xml.gz | 6.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5777 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5777 | 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_5777.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 in complex with capsaicin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: emd 5777 additional 1.map
ファイル | emd_5777_additional_1.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 capsaicin
全体 | 名称: Rat TRPV1 in complex with capsaicin |
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要素 |
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-超分子 #1000: Rat TRPV1 in complex with capsaicin
超分子 | 名称: Rat TRPV1 in complex with capsaicin / 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: Transient receptor potential cation channel subfamily V member 1 |
-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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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. |
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 FIELD / 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 |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
詳細 | 3D classification, refinement, and reconstruction were performed using RELION. |
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CTF補正 | 詳細: Each particle |
最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 4.2 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: 33238 |