+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5ndd | ||||||
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タイトル | Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in complex with AZ8838 at 2.8 angstrom resolution | ||||||
要素 | Lysozyme,Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2 | ||||||
キーワード | MEMBRANE PROTEIN / GPCR / 7TM | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of neutrophil mediated killing of gram-negative bacterium / potassium channel activating, G protein-coupled receptor signaling pathway / positive regulation of renin secretion into blood stream / positive regulation of eosinophil degranulation / leukocyte proliferation / mature conventional dendritic cell differentiation / regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of glomerular filtration / negative regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 3 signaling pathway ...positive regulation of neutrophil mediated killing of gram-negative bacterium / potassium channel activating, G protein-coupled receptor signaling pathway / positive regulation of renin secretion into blood stream / positive regulation of eosinophil degranulation / leukocyte proliferation / mature conventional dendritic cell differentiation / regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of glomerular filtration / negative regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 3 signaling pathway / thrombin-activated receptor activity / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of actin filament depolymerization / cell-cell junction maintenance / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of cytokine production involved in immune response / T cell activation involved in immune response / positive regulation of pseudopodium assembly / negative regulation of chemokine production / positive regulation of phagocytosis, engulfment / positive regulation of chemotaxis / negative regulation of JNK cascade / neutrophil activation / establishment of endothelial barrier / regulation of canonical NF-kappaB signal transduction / positive regulation of positive chemotaxis / positive regulation of leukocyte chemotaxis / positive regulation of Rho protein signal transduction / leukocyte migration / regulation of blood coagulation / pseudopodium / positive regulation of interleukin-10 production / regulation of JNK cascade / negative regulation of tumor necrosis factor-mediated signaling pathway / G-protein alpha-subunit binding / negative regulation of insulin secretion / positive regulation of chemokine production / viral release from host cell by cytolysis / peptidoglycan catabolic process / Peptide ligand-binding receptors / positive regulation of superoxide anion generation / positive regulation of GTPase activity / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / G protein-coupled receptor activity / electron transport chain / positive regulation of JNK cascade / vasodilation / positive regulation of interleukin-6 production / G-protein beta-subunit binding / positive regulation of type II interferon production / blood coagulation / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / protease binding / host cell cytoplasm / periplasmic space / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / defense response to bacterium / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / innate immune response / signaling receptor binding / heme binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Enterobacteria phage T4 (ファージ) Homo sapiens (ヒト) Escherichia coli (大腸菌) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.801 Å | ||||||
データ登録者 | Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. ...Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / Hermansson, N.-O. / Jazayeri, A. / Johansson, P. / Leong, L. / Prihandoko, R. / Rappas, M. / Soutter, H. / Snijder, A. / Sundstrom, L. / Tehan, B. / Thornton, P. / Troast, D. / Wiggin, G. / Zhukov, A. / Marshall, F.H. / Dekker, N. | ||||||
引用 | ジャーナル: Nature / 年: 2017 タイトル: Structural insight into allosteric modulation of protease-activated receptor 2. 著者: Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G.A. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / Hermansson, ...著者: Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G.A. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / Hermansson, N.O. / Jazayeri, A. / Johansson, P. / Leong, L. / Prihandoko, R. / Rappas, M. / Soutter, H. / Snijder, A. / Sundstrom, L. / Tehan, B. / Thornton, P. / Troast, D. / Wiggin, G. / Zhukov, A. / Marshall, F.H. / Dekker, N. | ||||||
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 | 5ndd.cif.gz | 129.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5ndd.ent.gz | 96.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5ndd.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 | 5ndd_validation.pdf.gz | 459.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5ndd_full_validation.pdf.gz | 462.8 KB | 表示 | |
XML形式データ | 5ndd_validation.xml.gz | 20.5 KB | 表示 | |
CIF形式データ | 5ndd_validation.cif.gz | 28.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/nd/5ndd ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5ndd | 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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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 69558.898 Da / 分子数: 1 変異: G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A,I289A, L293A 由来タイプ: 組換発現 由来: (組換発現) Enterobacteria phage T4 (ファージ), (組換発現) Homo sapiens (ヒト), (組換発現) Escherichia coli (大腸菌) 遺伝子: e, T4Tp126, F2RL1, GPR11, PAR2, cybC / プラスミド: pFASTBAC / 細胞株 (発現宿主): Sf9 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: D9IEF7, UniProt: P55085, UniProt: P0ABE7, UniProt: P00720*PLUS, lysozyme |
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#2: 化合物 | ChemComp-8TZ / (~{ |
#3: 化合物 | ChemComp-NA / |
#4: 化合物 | ChemComp-PO4 / |
#5: 水 | ChemComp-HOH / |
-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: 3.04 Å3/Da / 溶媒含有率: 59.52 % / 解説: Needle-shaped crystals (on average 0.1mm long) |
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結晶化 | 温度: 293 K / 手法: 脂質キュービック相法 / pH: 5.8 詳細: 0.1 M sodium citrate/citrate acid pH 5.5-6.2, 0.2 M ammonium phosphate dibasic, 38-43 % (w/v) PEG400 and 1 mM AZ8838 PH範囲: 5.5-6.2 / Temp details: Constant |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: Diamond / ビームライン: I24 / 波長: 0.96859 Å |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年6月5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: 0.96859 Å / 相対比: 1 |
反射 | 解像度: 2.8→34.34 Å / Num. obs: 17995 / % possible obs: 97.5 % / 冗長度: 3.4 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.11 / Net I/σ(I): 6.5 |
反射 シェル | 解像度: 2.8→2.95 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2671 / CC1/2: 0.692 / Rpim(I) all: 0.522 / % possible all: 98.9 |
-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: 3VW7 解像度: 2.801→34.336 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.92 / 位相誤差: 30.31
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.801→34.336 Å
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拘束条件 |
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LS精密化 シェル |
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