+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6z4s | ||||||
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タイトル | Crystal structure of the neurotensin receptor 1 (NTSR1-H4bmx) in complex with the small molecule inverse agonist SR48692 | ||||||
要素 | Neurotensin receptor type 1,DARPin,HRV 3C protease recognition sequence | ||||||
キーワード | MEMBRANE PROTEIN / GPCR ligand complex / NTSR1 / SR48692 / inverse agonist | ||||||
機能・相同性 | 機能・相同性情報 Peptide ligand-binding receptors / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / positive regulation of inhibitory postsynaptic potential / regulation of membrane depolarization / positive regulation of arachidonate secretion / L-glutamate import across plasma membrane ...Peptide ligand-binding receptors / G protein-coupled neurotensin receptor activity / inositol phosphate catabolic process / symmetric synapse / D-aspartate import across plasma membrane / positive regulation of gamma-aminobutyric acid secretion / positive regulation of inhibitory postsynaptic potential / regulation of membrane depolarization / positive regulation of arachidonate secretion / L-glutamate import across plasma membrane / neuron spine / regulation of respiratory gaseous exchange / positive regulation of glutamate secretion / negative regulation of systemic arterial blood pressure / negative regulation of release of sequestered calcium ion into cytosol / G alpha (q) signalling events / positive regulation of inositol phosphate biosynthetic process / temperature homeostasis / response to lipid / detection of temperature stimulus involved in sensory perception of pain / neuropeptide signaling pathway / axon terminus / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / learning / dendritic shaft / terminal bouton / cytoplasmic side of plasma membrane / perikaryon / dendritic spine / positive regulation of apoptotic process / membrane raft / axon / neuronal cell body / dendrite / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / identical protein binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) synthetic construct (人工物) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.707 Å | ||||||
データ登録者 | Deluigi, M. / Klipp, A. / Hilge, M. / Merklinger, L. / Klenk, C. / Plueckthun, A. | ||||||
資金援助 | スイス, 1件
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引用 | ジャーナル: Sci Adv / 年: 2021 タイトル: Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism. 著者: Deluigi, M. / Klipp, A. / Klenk, C. / Merklinger, L. / Eberle, S.A. / Morstein, L. / Heine, P. / Mittl, P.R.E. / Ernst, P. / Kamenecka, T.M. / He, Y. / Vacca, S. / Egloff, P. / Honegger, A. / Pluckthun, A. | ||||||
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 | 6z4s.cif.gz | 174.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6z4s.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6z4s.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 | 6z4s_validation.pdf.gz | 805 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6z4s_full_validation.pdf.gz | 806.9 KB | 表示 | |
XML形式データ | 6z4s_validation.xml.gz | 16.1 KB | 表示 | |
CIF形式データ | 6z4s_validation.cif.gz | 21.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/z4/6z4s ftp://data.pdbj.org/pub/pdb/validation_reports/z4/6z4s | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 53153.266 Da / 分子数: 1 変異: S83G,A86L,T101R,H103D,H105Y,L119F,M121L,R143K,A161V,R167L,R213L,V234L,K235R,V240L,I253A,I260A,N262R,K263R,H305R,C332V,F342A,T354S 由来タイプ: 組換発現 詳細: Residues 60-371 represent the rat neurotensin receptor 1 mutant H4bm (NTSR1-H4bm). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting ...詳細: Residues 60-371 represent the rat neurotensin receptor 1 mutant H4bm (NTSR1-H4bm). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting NTSR1 with the DARPin crystallisation chaperone. Residues 381 to 536 represent the DARPin crystallisation chaperone that is related to 5LW2. Residues 537 to 539 represent a short linker connecting the DARPin crystallisation chaperone with the HRV 3C protease recognition sequence. Residues 540 to 545 are part of the HRV 3C protease recognition sequence visible in the electron density.,Residues 60-371 represent the rat neurotensin receptor 1 mutant H4bm (NTSR1-H4bm). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting NTSR1 with the DARPin crystallisation chaperone. Residues 381 to 536 represent the DARPin crystallisation chaperone that is related to 5LW2. Residues 537 to 539 represent a short linker connecting the DARPin crystallisation chaperone with the HRV 3C protease recognition sequence. Residues 540 to 545 are part of the HRV 3C protease recognition sequence visible in the electron density.,Residues 60-371 represent the rat neurotensin receptor 1 mutant H4bm (NTSR1-H4bm). Residues 273 to 290 were deleted for crystallisation purposes. Residues 372 to 380 form a linker connecting NTSR1 with the DARPin crystallisation chaperone. Residues 381 to 536 represent the DARPin crystallisation chaperone that is related to 5LW2. Residues 537 to 539 represent a short linker connecting the DARPin crystallisation chaperone with the HRV 3C protease recognition sequence. Residues 540 to 545 are part of the HRV 3C protease recognition sequence visible in the electron density. 由来: (組換発現) Rattus norvegicus (ドブネズミ), (組換発現) synthetic construct (人工物) 遺伝子: Ntsr1, Ntsr / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P20789 |
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#2: 化合物 | ChemComp-Q6Q / |
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: 2.43 Å3/Da / 溶媒含有率: 49.44 % |
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結晶化 | 温度: 293.15 K / 手法: 脂質キュービック相法 詳細: 100 mM Na citrate 225-460 mM ammonium nitrate 30-32% (v/v) PEG400 1 uM SR48692 PH範囲: 4.8-51 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: Y |
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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: 1.000009 Å |
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年12月8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: 1.000009 Å / 相対比: 1 |
反射 | 解像度: 2.707→29.353 Å / Num. obs: 10475 / % possible obs: 90.6 % / 冗長度: 7.3 % / CC1/2: 0.964 / Rmerge(I) obs: 0.525 / Rpim(I) all: 0.198 / Rrim(I) all: 0.564 / Net I/σ(I): 4.3 |
反射 シェル | 解像度: 2.707→3.029 Å / Rmerge(I) obs: 4.678 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 524 / CC1/2: 0.294 / Rpim(I) all: 1.504 / Rrim(I) all: 4.929 |
Serial crystallography sample delivery | 手法: fixed target |
-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: 6YVR 解像度: 2.707→29.353 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.848 / WRfactor Rfree: 0.285 / WRfactor Rwork: 0.269 / SU B: 21.592 / SU ML: 0.412 / Average fsc free: 0.8505 / Average fsc work: 0.8675 / 交差検証法: FREE R-VALUE / ESU R Free: 0.523 / 詳細: Hydrogens have been added in their riding positions
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溶媒の処理 | イオンプローブ半径: 0.7 Å / 減衰半径: 0.7 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 38.575 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.707→29.353 Å
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拘束条件 |
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LS精密化 シェル |
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