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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7z3u | ||||||||||||||||||
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タイトル | Crystal structure of SARS-CoV-2 Main Protease after incubation with Sulfo-Calpeptin | ||||||||||||||||||
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![]() | HYDROLASE / main protease / MPro / cystein protease / drug development / drug target / peptide-like inhibitor / SARS-CoV-2 / COVID-19 | ||||||||||||||||||
機能・相同性 | ![]() protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | ![]() ![]() synthetic construct (人工物) | ||||||||||||||||||
手法 | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Reinke, P.Y.A. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Rahmani Mashhour, A. / Hauser, M. / Karnicar, K. / Usenik, A. / Lindic, N. ...Reinke, P.Y.A. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Rahmani Mashhour, A. / Hauser, M. / Karnicar, K. / Usenik, A. / Lindic, N. / Lach, M. / Boehler, H. / Beck, T. / Cox, R. / Chapman, H.N. / Hinrichs, W. / Turk, D. / Guenther, S. / Meents, A. | ||||||||||||||||||
資金援助 | ![]() ![]()
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![]() | ![]() タイトル: Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. 著者: Reinke, P.Y.A. / de Souza, E.E. / Gunther, S. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Herrmann, A. / Rahmani Mashhour, A. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. / ...著者: Reinke, P.Y.A. / de Souza, E.E. / Gunther, S. / Falke, S. / Lieske, J. / Ewert, W. / Loboda, J. / Herrmann, A. / Rahmani Mashhour, A. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. / Botosso, V.F. / Santelli, G.M.M. / Kapronezai, J. / de Araujo, M.V. / Silva-Pereira, T.T. / Filho, A.F.S. / Tavares, M.S. / Florez-Alvarez, L. / de Oliveira, D.B.L. / Durigon, E.L. / Giaretta, P.R. / Heinemann, M.B. / Hauser, M. / Seychell, B. / Bohler, H. / Rut, W. / Drag, M. / Beck, T. / Cox, R. / Chapman, H.N. / Betzel, C. / Brehm, W. / Hinrichs, W. / Ebert, G. / Latham, S.L. / Guimaraes, A.M.S. / Turk, D. / Wrenger, C. / Meents, A. #1: ![]() タイトル: Towards automated crystallographic structure refinement with phenix.refine. 著者: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 275 KB | 表示 | ![]() |
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PDB形式 | ![]() | 206.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 459.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 464.6 KB | 表示 | |
XML形式データ | ![]() | 28.8 KB | 表示 | |
CIF形式データ | ![]() | 42 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7qgwC ![]() 7qkaC ![]() 7qkbC ![]() 7qkcC ![]() 7z3tC ![]() 7z58C ![]() 8c3dC ![]() 6ynqS C: 同じ文献を引用 ( S: 精密化の開始モデル |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
-タンパク質 / タンパク質・ペプチド , 2種, 4分子 ABFG
#1: タンパク質 | 分子量: 33873.547 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: rep, 1a-1b / 発現宿主: ![]() ![]() #2: タンパク質・ペプチド | タイプ: Peptide-like / クラス: 阻害剤 / 分子量: 362.464 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (合成) synthetic construct (人工物) / 参照: BIRD: PRD_002387 |
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-非ポリマー , 4種, 440分子 ![](data/chem/img/DMS.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | #4: 化合物 | #5: 化合物 | #6: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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非ポリマーの詳細 | The bound form of calpeptin (RN2) in this entry was derived by incubation of MPro with the ...The bound form of calpeptin (RN2) in this entry was derived by incubation of MPro with the precursor Sulfo-Calpeptin, a modified form of calpeptin that is sulfonated at its C-terminus to mask the aldehyde group. |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.54 Å3/Da / 溶媒含有率: 51.62 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法 詳細: Co-crystallization with the compound was achieved by equlibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl against a ...詳細: Co-crystallization with the compound was achieved by equlibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ratio of malonic acid, imidazole, and boric acid), pH 7.5, containing 25% v/v PEG 1500 and 5% v/v DMSO. Prior to crystallization compound solutions in DMSO were dried onto the wells of SwissCI 96-well plates. To achieve reproducible crystal growth seeding was used. Crystals appeared within a few hours and reached their final size after 2 -3 days. Crystals were manually harvested and flash cooled in liquid nitrogen for subsequent X-ray diffraction data collection. |
-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: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS EIGER2 S 16M / 検出器: PIXEL / 日付: 2021年5月7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: 1.033 Å / 相対比: 1 |
反射 | 解像度: 1.72→49.22 Å / Num. obs: 74689 / % possible obs: 99.7 % / 冗長度: 7.5 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1086 / Net I/σ(I): 12.54 |
反射 シェル | 解像度: 1.72→1.782 Å / 冗長度: 7.7 % / Rmerge(I) obs: 2.172 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 7314 / CC1/2: 0.524 / CC star: 0.829 / Rpim(I) all: 0.8283 / Rrim(I) all: 2.328 / % possible all: 98.31 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 6YNQ 解像度: 1.72→49.22 Å / SU ML: 0.2558 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 28.6145 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 38.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.72→49.22 Å
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拘束条件 |
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LS精密化 シェル |
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