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TitleStructural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 4198, Year 2023
Publish dateJul 14, 2023
AuthorsSaya 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 AbstractSARS-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.
External linksNat Commun / PubMed:37452031 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.2 - 4.2 Å
Structure data

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
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-33821: SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 1)
Method: EM (single particle) / Resolution: 4.0 Å

33822

7yh7

EMDB-33822, PDB-7yh7:
SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-33823: SARS-CoV-2 spike in complex with neutralizing antibody NIV-10 focused on RBD and NIV-10 interface
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-33824: SARS-CoV-2 spike in complex with neutralizing antibody NIV-10 (state 1)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-33825: SARS-CoV-2 spike in complex with neutralizing antibody NIV-10 (state 2)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-33826: SARS-CoV-2 spike in complex with neutralizing antibody NIV-10 (state 3)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-33827: SARS-CoV-2 spike in complex with neutralizing antibody NIV-13 focused on RBD and NIV-13 interface
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-33828: SARS-CoV-2 spike in complex with neutralizing antibody NIV-13 (state 1)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-33829: SARS-CoV-2 spike in complex with neutralizing antibody NIV-13 (state 2)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-33830: SARS-CoV-2 spike in complex with neutralizing antibody NIV-13 (state 3)
Method: EM (single particle) / Resolution: 3.3 Å

34741

8hgl

EMDB-34741, PDB-8hgl:
SARS-CoV-2 spike in complex with neutralizing antibody NIV-11
Method: EM (single particle) / Resolution: 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
Method: EM (single particle) / Resolution: 3.4 Å

PDB-8hes:
Crystal structure of SARS-CoV-2 RBD and NIV-10 complex
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / virus / SARS-CoV-2 / RBD / spike / antibody / IgG / neutralizing antibody

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