+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-41864 | |||||||||
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タイトル | TRPV1 in nanodisc bound with empty vanilloid binding pocket at 4C | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | TRPV1 in nanodisc bound with empty vanilloid binding pocket at 4C / MEMBRANE PROTEIN | |||||||||
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 / phosphoprotein binding / calcium ion transmembrane transport / 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 / 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: 2.9 Å | |||||||||
データ登録者 | Arnold WR / Julius D / Cheng Y | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 タイトル: Structural basis of TRPV1 modulation by endogenous bioactive lipids. 著者: William R Arnold / Adamo Mancino / Frank R Moss / Adam Frost / David Julius / Yifan Cheng / 要旨: TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for ...TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for deciphering lipid modulation, which is relevant to understanding how pro-algesic agents enhance channel activity in the setting of inflammatory pain. Identification of a pocket within the TRPV1 transmembrane core has provided initial clues as to how phosphoinositide lipids bind to and regulate the channel. Here we show that this regulatory pocket in rat TRPV1 can accommodate diverse lipid species, including the inflammatory lipid lysophosphatidic acid, whose actions are determined by their specific modes of binding. Furthermore, we show that an empty-pocket channel lacking an endogenous phosphoinositide lipid assumes an agonist-like state, even at low temperature, substantiating the concept that phosphoinositide lipids serve as negative TRPV1 modulators whose ejection from the binding pocket is a critical step toward activation by thermal or chemical stimuli. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_41864.map.gz | 248.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-41864-v30.xml emd-41864.xml | 14.8 KB 14.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_41864_fsc.xml | 13.7 KB | 表示 | FSCデータファイル |
画像 | emd_41864.png | 72.6 KB | ||
Filedesc metadata | emd-41864.cif.gz | 5.8 KB | ||
その他 | emd_41864_half_map_1.map.gz emd_41864_half_map_2.map.gz | 254.9 MB 254.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-41864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41864 | HTTPS FTP |
-関連構造データ
関連構造データ | 8u3jMC 8t0cC 8t0eC 8t0yC 8t10C 8t3lC 8t3mC 8u2zC 8u30C 8u3aC 8u3cC 8u3lC 8u43C 8u4dC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_41864.map.gz / 形式: CCP4 / 大きさ: 274.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.68 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: #2
ファイル | emd_41864_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_41864_half_map_2.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 : TRPV1 in nanodisc with empty vanilloid binding pocket at 4C
全体 | 名称: TRPV1 in nanodisc with empty vanilloid binding pocket at 4C |
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要素 |
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-超分子 #1: TRPV1 in nanodisc with empty vanilloid binding pocket at 4C
超分子 | 名称: TRPV1 in nanodisc with empty vanilloid binding pocket at 4C タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 688 KDa |
-分子 #1: Transient receptor potential cation channel subfamily V member 1
分子 | 名称: Transient receptor potential cation channel subfamily V member 1 タイプ: protein_or_peptide / ID: 1 / コピー数: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 61.557422 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: SYYKGQTALH IAIERRNMTL VTLLVENGAD VQAAANGDFF KKTKGRPGFY FGELPLSLAA CTNQLAIVKF LLQNSWQPAD ISARDSVGN TVLHALVEVA DNTVDNTKFV TSMYNEILIL GAKLHPTLKL EEITNRKGLT PLALAASSGK IGVLAYILQR E IHEPECRH ...文字列: SYYKGQTALH IAIERRNMTL VTLLVENGAD VQAAANGDFF KKTKGRPGFY FGELPLSLAA CTNQLAIVKF LLQNSWQPAD ISARDSVGN TVLHALVEVA DNTVDNTKFV TSMYNEILIL GAKLHPTLKL EEITNRKGLT PLALAASSGK IGVLAYILQR E IHEPECRH LSRKFTEWAY GPVHSSLYDL SCIDTCEKNS VLEVIAYSSS ETPNRHDMLL VEPLNRLLQD KWDRFVKRIF YF NFFVYCL YMIIFTAAAY YRPVEGLPPY KLKNTVGDYF RVTGEILSVS GGVYFFFRGI QYFLQRRPSL KSLFVDSYSE ILF FVQSLF MLVSVVLYFS QRKEYVASMV FSLAMGWTNM LYYTRGFQQM GIYAVMIEKM ILRDLCRFMF VYLVFLFGFS TAVV TLIED GKYNSLYSTC LELFKFTIGM GDLEFTENYD FKAVFIILLL AYVILTYILL LNMLIALMGE TVNKIAQESK NIWKL QRAI TILDTEKSFL KCMRKAFRSG KLLQVGFTPD GKDDYRWCFR VDEVNWTTWN UniProtKB: Transient receptor potential cation channel subfamily V member 1 |
-分子 #2: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
分子 | 名称: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / タイプ: ligand / ID: 2 / コピー数: 4 / 式: 3PH |
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分子量 | 理論値: 704.998 Da |
Chemical component information | ChemComp-3PH: |
-分子 #3: SODIUM ION
分子 | 名称: SODIUM ION / タイプ: ligand / ID: 3 / コピー数: 1 |
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分子量 | 理論値: 22.99 Da |
-分子 #4: water
分子 | 名称: water / タイプ: ligand / ID: 4 / コピー数: 4 / 式: HOH |
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分子量 | 理論値: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-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 | 2.1 mg/mL |
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緩衝液 | pH: 7.5 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |