+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j9j | ||||||
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タイトル | Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy | ||||||
要素 | Transient receptor potential cation channel subfamily V member 1 | ||||||
キーワード | MEMBRANE PROTEIN / alpha helical | ||||||
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 / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / TRP channels ...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 / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / TRP channels / cellular response to acidic pH / excitatory extracellular ligand-gated monoatomic ion channel activity / thermoception / fever generation / 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 / extracellular ligand-gated monoatomic ion channel activity / cellular response to ATP / negative regulation of heart rate / temperature homeostasis / response to pain / cellular response to alkaloid / behavioral response to pain / diet induced thermogenesis / 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 / calcium ion import across plasma membrane / monoatomic cation channel activity / monoatomic ion transmembrane transport / sensory perception of pain / response to organonitrogen compound / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / calcium ion transmembrane transport / phosphoprotein binding / microglial cell activation / calcium channel activity / lipid metabolic process / cellular response to growth factor stimulus / response to peptide hormone / transmembrane signaling receptor activity / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cellular response to tumor necrosis factor / cellular response to heat / positive regulation of cytosolic calcium ion concentration / 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 | Wang, R.Y.-R. / Barad, B.A. / Fraser, J.S. / DiMaio, F. | ||||||
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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Remark 0 | THIS ENTRY 3J9J CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-5778) DETERMINED ...THIS ENTRY 3J9J CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-5778) DETERMINED ORIGINALLY BY AUTHORS: M.LIAO, E.CAO, D.JULIUS, Y.CHENG |
-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 | 3j9j.cif.gz | 440.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j9j.ent.gz | 349.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j9j.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 | 3j9j_validation.pdf.gz | 937.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j9j_full_validation.pdf.gz | 943.3 KB | 表示 | |
XML形式データ | 3j9j_validation.xml.gz | 35.6 KB | 表示 | |
CIF形式データ | 3j9j_validation.cif.gz | 52 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j9/3j9j ftp://data.pdbj.org/pub/pdb/validation_reports/j9/3j9j | HTTPS FTP |
-関連構造データ
関連構造データ | 5778M M: このデータのモデリングに利用したマップデータ |
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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: 67234.953 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) / 細胞株 (発現宿主): HEK293S / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O35433 配列の詳細 | PROTEIN CONSTRUCT COMPRISES UNP RESIDUES 111-603 AND 627-719. | |
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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 |
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緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE |
-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 |
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 / 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 |
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) |
-解析
対称性 | 点対称性: C4 (4回回転対称) | ||||||||||||
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3次元再構成 | 解像度: 3.275 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 35645 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / 対称性のタイプ: POINT | ||||||||||||
精密化ステップ | サイクル: LAST
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