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TitleOrphan broadly RBD-binding antibodies annotate three remaining conserved RBD epitopes along SARS-CoV-2 evolution.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 10566, Year 2025
Publish dateNov 26, 2025
AuthorsMinxiang Xie / Yinong Qiu / Xiaoyu Zhao / Jialu Shi / Yuanchen Liu / Qingsong Zhang / Jiaying He / Jiayan Li / Luotian Liu / Siyuan Sun / Yuzhen Zhu / Qiyu Mao / Yiming Long / Thiago Y Oliveira / Zijun Wang / Yunjiao Zhou / Yan Yan / Anqi Xia / Wenjing Zai / Christian T Mayer / Youhua Xie / Shibo Jiang / Lu Lu / Rong Xia / Fan Wu / Lei Sun / Pengfei Wang / Hin Chu / Qiao Wang /
PubMed AbstractThe receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein continues to evolve, facilitating antibody evasion. It remains unclear whether any conserved RBD epitopes persist across SARS-CoV- ...The receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein continues to evolve, facilitating antibody evasion. It remains unclear whether any conserved RBD epitopes persist across SARS-CoV-2 variants and whether vaccination and/or breakthrough infection (BTI) can elicit antibodies capable of targeting these conserved regions to counter future variants. Here, using a heterogeneous double-bait single B-cell sorting strategy, we identify a subset of antibodies with broad-spectrum RBD binding, including recognition of SARS-CoV-1 and emerging variants such as EG.5.1, BA.2.86, JN.1, and KP.2/3. These broadly binding antibodies (bbAbs) exhibit elevated levels of somatic hypermutation but are infrequently derived from clonally expanded B lymphocytes. Passive transfer of representative bbAbs reduces viral infection in a male hamster model. Structural analyses reveals that these bbAbs primarily target three distinct, highly conserved RBD epitopes, suggesting potential regions of future mutational pressure and highlighting the presence of conserved and immunogenic RBD conformations that may serve as a foundation for the development of broadly protective vaccines.
External linksNat Commun / PubMed:41298374 / PubMed Central
MethodsEM (single particle)
Resolution2.95 - 4.16 Å
Structure data

62660

9kzd

EMDB-62660, PDB-9kzd:
The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-171
Method: EM (single particle) / Resolution: 3.65 Å

62661

9kze

EMDB-62661, PDB-9kze:
The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-183
Method: EM (single particle) / Resolution: 3.4 Å

62680

9kzz

EMDB-62680, PDB-9kzz:
Structure of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-171
Method: EM (single particle) / Resolution: 3.18 Å

62687

9l05

EMDB-62687, PDB-9l05:
The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-198
Method: EM (single particle) / Resolution: 3.24 Å

62691

9l07

EMDB-62691, PDB-9l07:
The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-203
Method: EM (single particle) / Resolution: 3.28 Å

EMDB-62729: Raw consensus map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-203
Method: EM (single particle) / Resolution: 2.95 Å

EMDB-62731: Focused refinement up-RBD1 of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-203
Method: EM (single particle) / Resolution: 4.06 Å

EMDB-62733: Focused refinement up-RBD2 of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-203
Method: EM (single particle) / Resolution: 4.16 Å

62734

9l15

EMDB-62734, PDB-9l15:
Structure of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-203
Method: EM (single particle) / Resolution: 2.95 Å

EMDB-62744: Raw consensus map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-198
Method: EM (single particle) / Resolution: 3.08 Å

EMDB-62745: Focused refinement trimer1 of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-198
Method: EM (single particle) / Resolution: 2.98 Å

EMDB-62746: Focused refinement trimer2 of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-198
Method: EM (single particle) / Resolution: 3.43 Å

62777

9l2l

EMDB-62777, PDB-9l2l:
Structure of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-198
Method: EM (single particle) / Resolution: 2.98 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-antibody complex / VIRAL PROTEIN-IMMUNE SYSTEM complex

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