+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j9p | ||||||
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タイトル | Structure of the TRPA1 ion channel determined by electron cryo-microscopy | ||||||
要素 | Maltose-binding periplasmic protein, Transient receptor potential cation channel subfamily A member 1 chimera | ||||||
キーワード | TRANSPORT PROTEIN (運搬体タンパク質) / TRPA1 / TRP / transient / potential / receptor (受容体) / ion channel (イオンチャネル) / membrane protein (膜タンパク質) | ||||||
機能・相同性 | 機能・相同性情報 temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRPチャネル / channel activity / response to pain / cellular response to organic substance / detection of maltose stimulus / maltose binding ...temperature-gated cation channel activity / stereocilium bundle / detection of chemical stimulus involved in sensory perception of pain / thermoception / TRPチャネル / channel activity / response to pain / cellular response to organic substance / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / intracellularly gated calcium channel activity / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / detection of mechanical stimulus involved in sensory perception of pain / monoatomic ion transport / sensory perception of pain / response to cold / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / response to organic substance / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / response to organic cyclic compound / cellular response to hydrogen peroxide / outer membrane-bounded periplasmic space / protein homotetramerization / ペリプラズム / cell surface receptor signaling pathway / response to xenobiotic stimulus / DNA damage response / 生体膜 / identical protein binding / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | Escherichia coli (大腸菌) Homo sapiens (ヒト) | ||||||
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: 4.24 Å | ||||||
データ登録者 | Paulsen, C.E. / Armache, J.-P. / Gao, Y. / Cheng, Y. / Julius, D. | ||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: Structure of the TRPA1 ion channel suggests regulatory mechanisms. 著者: Candice E Paulsen / Jean-Paul Armache / Yuan Gao / Yifan Cheng / David Julius / 要旨: The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. ...The TRPA1 ion channel (also known as the wasabi receptor) is a detector of noxious chemical agents encountered in our environment or produced endogenously during tissue injury or drug metabolism. These include a broad class of electrophiles that activate the channel through covalent protein modification. TRPA1 antagonists hold potential for treating neurogenic inflammatory conditions provoked or exacerbated by irritant exposure. Despite compelling reasons to understand TRPA1 function, structural mechanisms underlying channel regulation remain obscure. Here we use single-particle electron cryo- microscopy to determine the structure of full-length human TRPA1 to ∼4 Å resolution in the presence of pharmacophores, including a potent antagonist. Several unexpected features are revealed, including an extensive coiled-coil assembly domain stabilized by polyphosphate co-factors and a highly integrated nexus that converges on an unpredicted transient receptor potential (TRP)-like allosteric domain. These findings provide new insights into the mechanisms of TRPA1 regulation, and establish a blueprint for structure-based design of analgesic and anti-inflammatory agents. | ||||||
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 | 3j9p.cif.gz | 460.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j9p.ent.gz | 312.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j9p.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/j9/3j9p ftp://data.pdbj.org/pub/pdb/validation_reports/j9/3j9p | HTTPS FTP |
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-関連構造データ
関連構造データ | 6267MC 6268C 6269C 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 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10024 (タイトル: Human TRPA1 ion channel with agonist AITC / Data size: 453.0 Data #1: TRP ion channel dataset [picked particles - single frame - processed]) |
-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: 172575.562 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) Escherichia coli, Homo sapiens / 遺伝子: malE, ANKTM1, TRPA1 / 細胞株 (発現宿主): HEK293 GnTi- / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0AEX9, UniProt: O75762 配列の詳細 | PROTEIN IS A CHIMERA COMPRISING | |
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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: Recombinant human TRPA1 ion channel / タイプ: COMPLEX |
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緩衝液 | 名称: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6 / pH: 8 / 詳細: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, 1 mM IP6 |
試料 | 濃度: 0.5 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 holey carbon |
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / Temp: 120 K / 湿度: 100 % 詳細: Blot for 7 seconds before plunging into liquid ethane (FEI VITROBOT MARK I). 手法: Blot for 7 seconds before plunging. |
-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: 2014年7月18日 詳細: Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods. |
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): 2800 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2 mm |
試料ホルダ | 温度: 120 K |
撮影 | 電子線照射量: 21 e/Å2 / フィルム・検出器のモデル: GATAN K2 (4k x 4k) 詳細: Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods. |
画像スキャン | デジタル画像の数: 1160 |
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: 4.24 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 43585 / 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 / 対称性のタイプ: POINT | ||||||||||||
精密化ステップ | サイクル: LAST
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