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TitleAn unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike.
Journal, issue, pagesCell Rep, Vol. 43, Issue 6, Page 114265, Year 2024
Publish dateMay 27, 2024
AuthorsBanghui Liu / Xuefeng Niu / Yijun Deng / Zhaoyong Zhang / Yanqun Wang / Xijie Gao / Huan Liang / Zimu Li / Qian Wang / Yuanyi Cheng / Qiuluan Chen / Shuangshuang Huang / Yingxian Pan / Mengzhen Su / Xiancheng Lin / Chuanying Niu / Yinglin Chen / Wenyi Yang / Yudi Zhang / Qihong Yan / Jun He / Jincun Zhao / Ling Chen / Xiaoli Xiong /
PubMed AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein continues to evolve antigenically, impacting antibody immunity. D1F6, an affinity-matured non-stereotypic VH1-2 ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein continues to evolve antigenically, impacting antibody immunity. D1F6, an affinity-matured non-stereotypic VH1-2 antibody isolated from a patient infected with the SARS-CoV-2 ancestral strain, effectively neutralizes most Omicron variants tested, including XBB.1.5. We identify that D1F6 in the immunoglobulin G (IgG) form is able to overcome the effect of most Omicron mutations through its avidity-enhanced multivalent S-trimer binding. Cryo-electron microscopy (cryo-EM) and biochemical analyses show that three simultaneous epitope mutations are generally needed to substantially disrupt the multivalent S-trimer binding by D1F6 IgG. Antigenic mutations at spike positions 346, 444, and 445, which appeared in the latest variants, have little effect on D1F6 binding individually. However, these mutations are able to act synergistically with earlier Omicron mutations to impair neutralization by affecting the interaction between D1F6 IgG and the S-trimer. These results provide insight into the mechanism by which accumulated antigenic mutations facilitate evasion of affinity-matured antibodies.
External linksCell Rep / PubMed:38805396
MethodsEM (single particle)
Resolution3.67 - 7.82 Å
Structure data

39916

8zby

EMDB-39916, PDB-8zby:
SARS-CoV-2 Omicron BA.1 spike trimer (x2-4P) in complex with 3 D1F6 Fabs (0 RBD up)
Method: EM (single particle) / Resolution: 3.67 Å

39917

8zbz

EMDB-39917, PDB-8zbz:
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)
Method: EM (single particle) / Resolution: 4.71 Å

39918

8zc0

EMDB-39918, PDB-8zc0:
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
Method: EM (single particle) / Resolution: 4.17 Å

39919

8zc1

EMDB-39919, PDB-8zc1:
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region
Method: EM (single particle) / Resolution: 4.17 Å

39920

8zc2

EMDB-39920, PDB-8zc2:
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate
Method: EM (single particle) / Resolution: 7.82 Å

39921

8zc3

EMDB-39921, PDB-8zc3:
SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)
Method: EM (single particle) / Resolution: 4.69 Å

39922

8zc4

EMDB-39922, PDB-8zc4:
SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
Method: EM (single particle) / Resolution: 3.95 Å

39923

8zc5

EMDB-39923, PDB-8zc5:
SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region
Method: EM (single particle) / Resolution: 3.91 Å

39924

8zc6

EMDB-39924, PDB-8zc6:
SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate
Method: EM (single particle) / Resolution: 6.85 Å

Chemicals

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

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Spike protein / Antibody Fab fragment / Complex / VIRAL PROTEIN-IMMUNE SYSTEM complex

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