+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j5p | ||||||
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タイトル | Structure of TRPV1 ion channel determined by single particle electron cryo-microscopy | ||||||
要素 | Transient receptor potential cation channel subfamily V member 1 | ||||||
キーワード | TRANSPORT PROTEIN / TRPV1 channel | ||||||
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 | 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: 3.275 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: Structure of the TRPV1 ion channel determined by electron cryo-microscopy. 著者: Maofu Liao / Erhu Cao / David Julius / Yifan Cheng / 要旨: Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been ...Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4 Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (S5-S6) and the intervening pore loop, which is flanked by S1-S4 voltage-sensor-like domains. TRPV1 has a wide extracellular 'mouth' with a short selectivity filter. The conserved 'TRP domain' interacts with the S4-S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function. | ||||||
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 | 3j5p.cif.gz | 416.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j5p.ent.gz | 337.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j5p.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 | 3j5p_validation.pdf.gz | 921.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j5p_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 3j5p_validation.xml.gz | 100.3 KB | 表示 | |
CIF形式データ | 3j5p_validation.cif.gz | 144 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j5/3j5p ftp://data.pdbj.org/pub/pdb/validation_reports/j5/3j5p | HTTPS FTP |
-関連構造データ
関連構造データ | 5778MC 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-10005 (タイトル: TRPV1 dataset taken on a K2 direct electron detector Data size: 6.3 TB / Data #1: TRPV1 picked particles [tilt series] Data #2: TRPV1 raw multi-frame micrographs [micrographs - multiframe] Data #3: TRPV1 summed frame micrographs [micrographs - single frame]) |
-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: 68242.156 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 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 / 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: 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 FIELD / 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: 946 |
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: 3.275 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 35645 / 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. (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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