+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j5q | |||||||||
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タイトル | Structure of TRPV1 ion channel in complex with DkTx and RTX determined by single particle electron cryo-microscopy | |||||||||
要素 |
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キーワード | TRANSPORT PROTEIN/TOXIN / TRPV1 channel / DkTx / RTX / TRANSPORT PROTEIN-TOXIN complex | |||||||||
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 / negative regulation of mitochondrial membrane potential / detection of temperature stimulus involved in sensory perception of pain / calcium ion import across plasma membrane / 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 / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to heat / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / toxin activity / response to heat / 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) Chilobrachys guangxiensis (クモ) | |||||||||
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: 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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3j5q.cif.gz | 428.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j5q.ent.gz | 339 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j5q.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j5/3j5q ftp://data.pdbj.org/pub/pdb/validation_reports/j5/3j5q | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 70795.211 Da / 分子数: 4 / 断片: SEE REMARK 999 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Trpv1, Vr1, Vr1l / プラスミド: pFastBac1 / 細胞株 (発現宿主): HEK293S GnTI / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O35433 #2: タンパク質・ペプチド | 分子量: 3433.014 Da / 分子数: 4 / 断片: UNP residues 51-81 / 由来タイプ: 天然 / 由来: (天然) Chilobrachys guangxiensis (クモ) / 参照: UniProt: P0C247 配列の詳細 | THE TRPV1 CONSTRUCT COMPRISES RESIDUES 110-603 AND 627-764, WITH RESIDUES 604-626 DELETED. RESIDUES ...THE TRPV1 CONSTRUCT COMPRISES RESIDUES 110-603 AND 627-764, WITH RESIDUES 604-626 DELETED. RESIDUES 719-764 ARE NOT MODELED, WITH THE EXCEPTION OF 11 RESIDUES (NUMBERED 752-762 IN THE COORDINATE | |
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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: Rat TRPV1 in complex with DkTx and resiniferatoxin / タイプ: COMPLEX / 詳細: Tetramer |
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分子量 | 値: 0.3 MDa / 実験値: NO |
緩衝液 | 名称: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP / pH: 7.4 / 詳細: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP |
試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: 400 mesh Quantifoil grid |
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / Temp: 120 K / 湿度: 90 % 詳細: Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III) 手法: Blot for 6 sec |
-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 / 日付: 2013年1月1日 詳細: Gatan K2 Summit operated in super-resolution counting mode, image recorded with dose fractionation method. |
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 FIELDBright-field microscopy / 倍率(公称値): 31000 X / 倍率(補正後): 31000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2 mm / カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: OTHER / 資料ホルダタイプ: FEI Polara cartridge |
撮影 | 電子線照射量: 21 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 詳細: Operated in super-resolution counting mode, dose fractionation |
画像スキャン | デジタル画像の数: 900 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア | 名称: RELION / カテゴリ: 3次元再構成 | ||||||||||||
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CTF補正 | 詳細: Each particle | ||||||||||||
対称性 | 点対称性: C4 (4回回転対称) | ||||||||||||
3次元再構成 | 手法: Maximum likelihood / 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 36158 / ピクセルサイズ(公称値): 1.2156 Å / ピクセルサイズ(実測値): 1.2156 Å 詳細: The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental ...詳細: The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental density. Interatomic clashes between the ankyrin repeats and the C-terminal beta sheet are the result of poor geometry due to relatively poor experimental density in these regions. Resolution and averaging of DkTx density was insufficient to provide side chain geometry. The DkTx model was generated as a poly-ALA model based on hanatoxin (PDB entry 1D1H) and docked into the DkTx density with slight modification. (Single particle details: 3D classification, refinement, and reconstruction were performed using RELION) (Single particle--Applied symmetry: C4) Refinement type: HALF-MAPS REFINED INDEPENDENTLY / 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: REAL 詳細: REFINEMENT PROTOCOL--de novo model building DETAILS--The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are ...詳細: REFINEMENT PROTOCOL--de novo model building DETAILS--The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental density. | ||||||||||||
精密化ステップ | サイクル: LAST
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