EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
ジャーナル・号・ページ	Nat Commun, Vol. 14, Issue 1, Page 4198, Year 2023
掲載日	2023年7月14日
著者	Saya Moriyama / Yuki Anraku / Shunta Taminishi / Yu Adachi / Daisuke Kuroda / Shunsuke Kita / Yusuke Higuchi / Yuhei Kirita / Ryutaro Kotaki / Keisuke Tonouchi / Kohei Yumoto / Tateki Suzuki / Taiyou Someya / Hideo Fukuhara / Yudai Kuroda / Tsukasa Yamamoto / Taishi Onodera / Shuetsu Fukushi / Ken Maeda / Fukumi Nakamura-Uchiyama / Takao Hashiguchi / Atsushi Hoshino / Katsumi Maenaka / Yoshimasa Takahashi /
PubMed 要旨	SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies ...SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.
リンク	Nat Commun / PubMed:37452031 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.2 - 4.2 Å
構造データ	33820 7yh6 EMDB-33820: SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 focused on RBD and NIV-8 interface PDB-7yh6: Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8 手法: EM (単粒子) / 解像度: 3.4 Å EMDB-33821: SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 1) 手法: EM (単粒子) / 解像度: 4.0 Å 33822 7yh7 EMDB-33822, PDB-7yh7: SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2) 手法: EM (単粒子) / 解像度: 3.3 Å EMDB-33823: SARS-CoV-2 spike in complex with neutralizing antibody NIV-10 focused on RBD and NIV-10 interface 手法: EM (単粒子) / 解像度: 4.2 Å EMDB-33824: SARS-CoV-2 spike in complex with neutralizing antibody NIV-10 (state 1) 手法: EM (単粒子) / 解像度: 3.0 Å EMDB-33825: SARS-CoV-2 spike in complex with neutralizing antibody NIV-10 (state 2) 手法: EM (単粒子) / 解像度: 3.2 Å EMDB-33826: SARS-CoV-2 spike in complex with neutralizing antibody NIV-10 (state 3) 手法: EM (単粒子) / 解像度: 3.4 Å EMDB-33827: SARS-CoV-2 spike in complex with neutralizing antibody NIV-13 focused on RBD and NIV-13 interface 手法: EM (単粒子) / 解像度: 4.0 Å EMDB-33828: SARS-CoV-2 spike in complex with neutralizing antibody NIV-13 (state 1) 手法: EM (単粒子) / 解像度: 3.2 Å EMDB-33829: SARS-CoV-2 spike in complex with neutralizing antibody NIV-13 (state 2) 手法: EM (単粒子) / 解像度: 3.4 Å EMDB-33830: SARS-CoV-2 spike in complex with neutralizing antibody NIV-13 (state 3) 手法: EM (単粒子) / 解像度: 3.3 Å 34741 8hgl EMDB-34741, PDB-8hgl: SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 手法: EM (単粒子) / 解像度: 2.9 Å 34742 8hgm EMDB-34742: SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 focused on RBD and NIV-11 interface PDB-8hgm: Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11 手法: EM (単粒子) / 解像度: 3.4 Å PDB-8hes: Crystal structure of SARS-CoV-2 RBD and NIV-10 complex 手法: X-RAY DIFFRACTION / 解像度: 2.2 Å
化合物	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-アセチル-β-D-グルコサミン / N-アセチルグルコサミン ChemComp-HOH: WATER / 水
由来	severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2) homo sapiens (ヒト)
キーワード	VIRAL PROTEIN/IMMUNE SYSTEM (ウイルス性) / Complex / VIRAL PROTEIN (ウイルスタンパク質) / VIRAL PROTEIN-IMMUNE SYSTEM complex (ウイルス性) / virus (ウイルス) / SARS-CoV-2 (SARSコロナウイルス2) / RBD / spike / antibody (抗体) / IgG / neutralizing antibody (中和抗体)