+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20702 | |||||||||
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タイトル | EMDB: Cryo electron microscopy map of the ATP-gated rat P2X7 ion channel in the apo, closed state | |||||||||
マップデータ | Overall map for the apo- (closed) state of rat P2X7 receptor | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Platelet homeostasis / The NLRP3 inflammasome / regulation of presynaptic dense core granule exocytosis / positive regulation of lymphocyte apoptotic process / positive regulation of bleb assembly / NAD transport / phagolysosome assembly / Elevation of cytosolic Ca2+ levels / phospholipid transfer to membrane / positive regulation of cytoskeleton organization ...Platelet homeostasis / The NLRP3 inflammasome / regulation of presynaptic dense core granule exocytosis / positive regulation of lymphocyte apoptotic process / positive regulation of bleb assembly / NAD transport / phagolysosome assembly / Elevation of cytosolic Ca2+ levels / phospholipid transfer to membrane / positive regulation of cytoskeleton organization / purinergic nucleotide receptor signaling pathway / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / lymphocyte apoptotic process / positive regulation of monoatomic ion transmembrane transport / gamma-aminobutyric acid secretion / pore complex assembly / positive regulation of interleukin-1 alpha production / plasma membrane organization / negative regulation of cell volume / positive regulation of gamma-aminobutyric acid secretion / ATP export / bleb / collagen metabolic process / plasma membrane phospholipid scrambling / response to fluid shear stress / T cell apoptotic process / positive regulation of prostaglandin secretion / bleb assembly / positive regulation of T cell apoptotic process / mitochondrial depolarization / vesicle budding from membrane / prostaglandin secretion / ceramide biosynthetic process / cellular response to dsRNA / programmed cell death / positive regulation of glutamate secretion / positive regulation of ossification / cell volume homeostasis / glutamate secretion / skeletal system morphogenesis / negative regulation of bone resorption / phospholipid translocation / positive regulation of macrophage cytokine production / positive regulation of calcium ion transport into cytosol / response to ATP / positive regulation of mitochondrial depolarization / response to zinc ion / T cell homeostasis / cellular response to organic cyclic compound / monoatomic cation transport / synaptic vesicle exocytosis / membrane depolarization / membrane protein ectodomain proteolysis / neuronal action potential / protein secretion / negative regulation of MAPK cascade / response to electrical stimulus / positive regulation of bone mineralization / response to mechanical stimulus / T cell proliferation / regulation of sodium ion transport / extrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / sensory perception of pain / positive regulation of glycolytic process / reactive oxygen species metabolic process / protein serine/threonine kinase activator activity / positive regulation of interleukin-1 beta production / mitochondrion organization / establishment of localization in cell / positive regulation of protein secretion / apoptotic signaling pathway / calcium ion transmembrane transport / lipopolysaccharide binding / response to bacterium / neuromuscular junction / cell morphogenesis / protein catabolic process / response to organic cyclic compound / terminal bouton / T cell mediated cytotoxicity / protein processing / positive regulation of interleukin-6 production / response to calcium ion / channel activity / positive regulation of T cell mediated cytotoxicity / calcium ion transport / MAPK cascade / cell-cell junction / nuclear envelope / signaling receptor activity / gene expression / scaffold protein binding / postsynapse / response to lipopolysaccharide / positive regulation of MAPK cascade / cell surface receptor signaling pathway / defense response to Gram-positive bacterium 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 | Mansoor SE / McCarthy AE | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Cell / 年: 2019 タイトル: Full-Length P2X Structures Reveal How Palmitoylation Prevents Channel Desensitization. 著者: Alanna E McCarthy / Craig Yoshioka / Steven E Mansoor / 要旨: P2X receptors are trimeric, non-selective cation channels activated by extracellular ATP. The P2X receptor subtype is a pharmacological target because of involvement in apoptotic, inflammatory, and ...P2X receptors are trimeric, non-selective cation channels activated by extracellular ATP. The P2X receptor subtype is a pharmacological target because of involvement in apoptotic, inflammatory, and tumor progression pathways. It is the most structurally and functionally distinct P2X subtype, containing a unique cytoplasmic domain critical for the receptor to initiate apoptosis and not undergo desensitization. However, lack of structural information about the cytoplasmic domain has hindered understanding of the molecular mechanisms underlying these processes. We report cryoelectron microscopy structures of full-length rat P2X receptor in apo and ATP-bound states. These structures reveal how one cytoplasmic element, the C-cys anchor, prevents desensitization by anchoring the pore-lining helix to the membrane with palmitoyl groups. They show a second cytoplasmic element with a unique fold, the cytoplasmic ballast, which unexpectedly contains a zinc ion complex and a guanosine nucleotide binding site. Our structures provide first insights into the architecture and function of a P2X receptor cytoplasmic domain. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_20702.map.gz | 117.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20702-v30.xml emd-20702.xml | 15.8 KB 15.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_20702_fsc.xml | 11.4 KB | 表示 | FSCデータファイル |
画像 | emd_20702.png | 116.1 KB | ||
その他 | emd_20702_additional_1.map.gz emd_20702_additional_2.map.gz | 117.2 MB 117.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20702 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20702 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_20702_validation.pdf.gz | 523.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_20702_full_validation.pdf.gz | 522.7 KB | 表示 | |
XML形式データ | emd_20702_validation.xml.gz | 12.1 KB | 表示 | |
CIF形式データ | emd_20702_validation.cif.gz | 16 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20702 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20702 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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-マップ
ファイル | ダウンロード / ファイル: emd_20702.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Overall map for the apo- (closed) state of rat P2X7 receptor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: Map for the apo- (closed) state of rat...
ファイル | emd_20702_additional_1.map | ||||||||||||
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注釈 | Map for the apo- (closed) state of rat P2X7 receptor from a focused refinement using a mask that includes the transmembrane domain and the cytoplasmic domain but excludes the extracellular domain. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Map for the apo- (closed) state of rat...
ファイル | emd_20702_additional_2.map | ||||||||||||
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注釈 | Map for the apo- (closed) state of rat P2X7 receptor from a focused refinement using a mask that includes the extracellular domain but excludes the transmembrane domain and the cytoplasmic domain | ||||||||||||
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 : P2X7 receptor ion channel
全体 | 名称: P2X7 receptor ion channel |
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要素 |
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-超分子 #1: P2X7 receptor ion channel
超分子 | 名称: P2X7 receptor ion channel / 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) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-分子 #1: P2X purinoceptor 7
分子 | 名称: P2X purinoceptor 7 / タイプ: protein_or_peptide / ID: 1 / コピー数: 3 / 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: 69.904016 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MPACCSWNDV FQYETNKVTR IQSVNYGTIK WILHMTVFSY VSFALMSDKL YQRKEPLISS VHTKVKGVAE VTENVTEGGV TKLVHGIFD TADYTLPLQG NSFFVMTNYL KSEGQEQKLC PEYPSRGKQC HSDQGCIKGW MDPQSKGIQT GRCIPYDQKR K TCEIFAWC ...文字列: MPACCSWNDV FQYETNKVTR IQSVNYGTIK WILHMTVFSY VSFALMSDKL YQRKEPLISS VHTKVKGVAE VTENVTEGGV TKLVHGIFD TADYTLPLQG NSFFVMTNYL KSEGQEQKLC PEYPSRGKQC HSDQGCIKGW MDPQSKGIQT GRCIPYDQKR K TCEIFAWC PAEEGKEAPR PALLRSAENF TVLIKNNIDF PGHNYTTRNI LPGMNISCTF HKTWNPQCPI FRLGDIFQEI GE NFTEVAV QGGIMGIEIY WDCNLDSWSH RCQPKYSFRR LDDKYTNESL FPGYNFRYAK YYKENGMEKR TLIKAFGVRF DIL VFGTGG KFDIIQLVVY IGSTLSYFGL ATVCIDLIIN TYASTCCRSR VYPSCKCCEP CAVNEYYYRK KCEPIVEPKP TLKY VSFVD EPHIWMVDQQ LLGKSLQDVK GQEVPRPQTD FLELSRLSLS LHHSPPIPGQ PEEMQLLQIE AVPRSRDSPD WCQCG NCLP SQLPENRRAL EELCCRRKPG QCITTSELFS KIVLSREALQ LLLLYQEPLL ALEGEAINSK LRHCAYRSYA TWRFVS QDM ADFAILPSCC RWKIRKEFPK TQGQYSGFKY PYSNSAVDAG LEVLFQ |
-分子 #4: GUANOSINE-5'-DIPHOSPHATE
分子 | 名称: GUANOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 4 / コピー数: 3 / 式: GDP |
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分子量 | 理論値: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-分子 #5: ZINC ION
分子 | 名称: ZINC ION / タイプ: ligand / ID: 5 / コピー数: 6 / 式: ZN |
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分子量 | 理論値: 65.409 Da |
-分子 #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 6 / コピー数: 9 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-分子 #7: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydr...
分子 | 名称: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine タイプ: ligand / ID: 7 / コピー数: 3 / 式: Q3G |
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分子量 | 理論値: 764.022 Da |
Chemical component information | ChemComp-Q3G: |
-分子 #8: PALMITIC ACID
分子 | 名称: PALMITIC ACID / タイプ: ligand / ID: 8 / コピー数: 18 / 式: PLM |
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分子量 | 理論値: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-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
緩衝液 | pH: 7 |
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グリッド | 詳細: unspecified |
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: FEI FALCON III (4k x 4k) 平均電子線量: 27.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |