+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7c8w | ||||||||||||
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タイトル | Structure of sybody MR17 in complex with the SARS-CoV-2 S receptor-binding domain (RBD) | ||||||||||||
要素 |
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キーワード | PROTEIN BINDING / coronavirus / Covid-19 / nanobody / neutralizing antibody / receptor binding protein / SARS-CoV-2 / S protein / synthetic antibody / VHH. | ||||||||||||
機能・相同性 | 機能・相同性情報 Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | synthetic construct (人工物) Severe acute respiratory syndrome coronavirus 2 (ウイルス) | ||||||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.77 Å | ||||||||||||
データ登録者 | Li, T. / Cai, H. / Yao, H. / Qin, W. / Li, D. | ||||||||||||
資金援助 | 中国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection. 著者: Tingting Li / Hongmin Cai / Hebang Yao / Bingjie Zhou / Ning Zhang / Martje Fentener van Vlissingen / Thijs Kuiken / Wenyu Han / Corine H GeurtsvanKessel / Yuhuan Gong / Yapei Zhao / Quan ...著者: Tingting Li / Hongmin Cai / Hebang Yao / Bingjie Zhou / Ning Zhang / Martje Fentener van Vlissingen / Thijs Kuiken / Wenyu Han / Corine H GeurtsvanKessel / Yuhuan Gong / Yapei Zhao / Quan Shen / Wenming Qin / Xiao-Xu Tian / Chao Peng / Yanling Lai / Yanxing Wang / Cedric A J Hutter / Shu-Ming Kuo / Juan Bao / Caixuan Liu / Yifan Wang / Audrey S Richard / Hervé Raoul / Jiaming Lan / Markus A Seeger / Yao Cong / Barry Rockx / Gary Wong / Yuhai Bi / Dimitri Lavillette / Dianfan Li / 要旨: SARS-CoV-2, the causative agent of COVID-19, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein. Neutralizing antibodies that block RBD-ACE2 interaction are candidates ...SARS-CoV-2, the causative agent of COVID-19, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (K = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC = 0.42 μg mL). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak. | ||||||||||||
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 | 7c8w.cif.gz | 95.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7c8w.ent.gz | 57.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7c8w.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 | 7c8w_validation.pdf.gz | 908.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7c8w_full_validation.pdf.gz | 911.7 KB | 表示 | |
XML形式データ | 7c8w_validation.xml.gz | 13.9 KB | 表示 | |
CIF形式データ | 7c8w_validation.cif.gz | 18 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/c8/7c8w ftp://data.pdbj.org/pub/pdb/validation_reports/c8/7c8w | 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: 抗体 | 分子量: 13433.839 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) |
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#2: タンパク質 | 分子量: 23747.643 Da / 分子数: 1 / Fragment: Receptor binding domain / 由来タイプ: 組換発現 由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス) 遺伝子: S, 2 / 細胞株 (発現宿主): Hi5 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P0DTC2 |
#3: 多糖 | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
#4: 化合物 | ChemComp-GOL / |
研究の焦点であるリガンドがあるか | Y |
Has protein modification | 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: 3.63 Å3/Da / 溶媒含有率: 66.07 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 0.2M magnesium formate dihydrate, 20% w/v polyethylene glycol 3350 |
-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: SSRF / ビームライン: BL19U1 / 波長: 0.97853 Å |
検出器 | タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2020年5月10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: 0.97853 Å / 相対比: 1 |
反射 | 解像度: 2.77→49.71 Å / Num. obs: 13308 / % possible obs: 100 % / 冗長度: 21 % / Biso Wilson estimate: 73.65 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.062 / Net I/σ(I): 11.1 |
反射 シェル | 解像度: 2.77→2.92 Å / 冗長度: 20.8 % / Rmerge(I) obs: 2.222 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1909 / CC1/2: 0.753 / Rpim(I) all: 0.494 / % possible all: 99.9 |
-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: 6M0J 解像度: 2.77→49.71 Å / SU ML: 0.424 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.4731 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: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 73.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.77→49.71 Å
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拘束条件 |
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LS精密化 シェル |
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