+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7p2l | |||||||||
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タイトル | thermostabilised 7TM domain of human mGlu5 receptor bound to photoswitchable ligand alloswitch-1 | |||||||||
要素 | Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5 | |||||||||
キーワード | SIGNALING PROTEIN / G protein coupled receptor (Gタンパク質共役受容体) / mGlu5 7TM / photoswitchable ligand / allosteric modulator (アロステリック調節因子) | |||||||||
機能・相同性 | 機能・相同性情報 A2A adenosine receptor binding / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / astrocyte projection / G protein-coupled glutamate receptor signaling pathway ...A2A adenosine receptor binding / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / astrocyte projection / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / protein kinase C-activating G protein-coupled receptor signaling pathway / glutamate receptor activity / Neurexins and neuroligins / protein tyrosine kinase activator activity / : / viral release from host cell by cytolysis / regulation of synaptic transmission, glutamatergic / peptidoglycan catabolic process / protein tyrosine kinase binding / locomotory behavior / dendritic shaft / 学習 / G protein-coupled receptor activity / postsynaptic density membrane / synapse organization / Schaffer collateral - CA1 synapse / 認識 / cellular response to amyloid-beta / cell wall macromolecule catabolic process / リゾチーム / lysozyme activity / G alpha (q) signalling events / chemical synaptic transmission / host cell cytoplasm / positive regulation of MAPK cascade / 樹状突起スパイン / learning or memory / defense response to bacterium / glutamatergic synapse / 樹状突起 / regulation of DNA-templated transcription / identical protein binding / 細胞膜 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) Enterobacteria phage T4 (ファージ) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.54 Å | |||||||||
データ登録者 | Huang, C.Y. / Vinothkumar, K.R. / Lebon, G. | |||||||||
資金援助 | フランス, 2件
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引用 | ジャーナル: Cell Rep / 年: 2021 タイトル: Agonists and allosteric modulators promote signaling from different metabotropic glutamate receptor 5 conformations. 著者: Chady Nasrallah / Giuseppe Cannone / Julie Briot / Karine Rottier / Alice E Berizzi / Chia-Ying Huang / Robert B Quast / Francois Hoh / Jean-Louis Banères / Fanny Malhaire / Ludovic Berto / ...著者: Chady Nasrallah / Giuseppe Cannone / Julie Briot / Karine Rottier / Alice E Berizzi / Chia-Ying Huang / Robert B Quast / Francois Hoh / Jean-Louis Banères / Fanny Malhaire / Ludovic Berto / Anaëlle Dumazer / Joan Font-Ingles / Xavier Gómez-Santacana / Juanlo Catena / Julie Kniazeff / Cyril Goudet / Amadeu Llebaria / Jean-Philippe Pin / Kutti R Vinothkumar / Guillaume Lebon / 要旨: Metabotropic glutamate receptors (mGluRs) are dimeric G-protein-coupled receptors activated by the main excitatory neurotransmitter, L-glutamate. mGluR activation by agonists binding in the venus ...Metabotropic glutamate receptors (mGluRs) are dimeric G-protein-coupled receptors activated by the main excitatory neurotransmitter, L-glutamate. mGluR activation by agonists binding in the venus flytrap domain is regulated by positive (PAM) or negative (NAM) allosteric modulators binding to the 7-transmembrane domain (7TM). We report the cryo-electron microscopy structures of fully inactive and intermediate-active conformations of mGlu receptor bound to an antagonist and a NAM or an agonist and a PAM, respectively, as well as the crystal structure of the 7TM bound to a photoswitchable NAM. The agonist induces a large movement between the subunits, bringing the 7TMs together and stabilizing a 7TM conformation structurally similar to the inactive state. Using functional approaches, we demonstrate that the PAM stabilizes a 7TM active conformation independent of the conformational changes induced by agonists, representing an alternative mode of mGlu activation. These findings provide a structural basis for different mGluR activation modes. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7p2l.cif.gz | 99.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7p2l.ent.gz | 72.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7p2l.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/p2/7p2l ftp://data.pdbj.org/pub/pdb/validation_reports/p2/7p2l | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 51918.055 Da / 分子数: 1 / 変異: E579A,N667Y,I669A,G675M,T742A,S753A / 由来タイプ: 組換発現 詳細: The macromolecule is a chimera of mGluR TMD and T4 lysozyme. The Uniprot ID of mGluR5 is P41594 and the T4 lysozyme if P00720. The lysozyme sequence is inserted between residue 678 and 679 of ...詳細: The macromolecule is a chimera of mGluR TMD and T4 lysozyme. The Uniprot ID of mGluR5 is P41594 and the T4 lysozyme if P00720. The lysozyme sequence is inserted between residue 678 and 679 of mGluR5. In the PDB, the lysozyme is numbered from 1002-1162 (Asn & Tyr). The gaps are between 680-688 and 721-728. Residues 644 & 733 form a disuphide bond. The lysozyme has also been engineered and has the following mutations. C54T (in PDB it is 1054) and C97T (in PDB it is 1097). 由来: (組換発現) Homo sapiens (ヒト), (組換発現) Enterobacteria phage T4 (ファージ) 遺伝子: GRM5, GPRC1E, MGLUR5 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P41594, UniProt: P00720, リゾチーム |
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#2: 化合物 | ChemComp-4YI / |
#3: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | Y |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.72 Å3/Da / 溶媒含有率: 54.83 % |
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結晶化 | 温度: 295 K / 手法: 脂質キュービック相法 詳細: 0.15-0.25 M ammonium phosphate dibasic, 22-24 % polyethylene glycol 400, either with 0.10 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.7-6.8 or 0.1 M HEPES pH 6.8 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: シンクロトロン / サイト: SLS / ビームライン: X06SA / 波長: 1 Å |
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年12月14日 |
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 | 波長: 1 Å / 相対比: 1 |
反射 | 解像度: 2.54→49.11 Å / Num. obs: 16595 / % possible obs: 100 % / 冗長度: 10.66 % / CC1/2: 0.997 / Rrim(I) all: 0.253 / Net I/σ(I): 6.35 |
反射 シェル | 解像度: 2.54→2.61 Å / 冗長度: 9.3 % / Num. unique obs: 1184 / CC1/2: 0.51 / Rrim(I) all: 2.685 / % possible all: 99 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4oo9 解像度: 2.54→49.11 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.881 / SU B: 17.497 / SU ML: 0.35 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.647 / ESU R Free: 0.336 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 149.46 Å2 / Biso mean: 69.807 Å2 / Biso min: 46.68 Å2
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精密化ステップ | サイクル: final / 解像度: 2.54→49.11 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.54→2.606 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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