8SDF image
Entry Detail
PDB ID:
8SDF
Keywords:
Title:
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.4
Biological Source:
PDB Version:
Deposition Date:
2023-04-06
Release Date:
2024-03-13
Method Details:
Experimental Method:
Resolution:
1.79 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Neutralizing antibody CC25.4 heavy chain
Chain IDs:B (auth: H), E (auth: B)
Chain Length:229
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Neutralizing antibody CC25.4 light chain
Chain IDs:C (auth: L), F (auth: C)
Chain Length:217
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:A (auth: Z), D (auth: A)
Chain Length:205
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Primary Citation
Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.
Biorxiv ? ? ? (2023)
PMID: 37162858 DOI: 10.1101/2023.04.26.538488

Abstact

Developing broad coronavirus vaccines requires identifying and understanding the molecular basis of broadly neutralizing antibody (bnAb) spike sites. In our previous work, we identified sarbecovirus spike RBD group 1 and 2 bnAbs. We have now shown that many of these bnAbs can still neutralize highly mutated SARS-CoV-2 variants, including the XBB.1.5. Structural studies revealed that group 1 bnAbs use recurrent germline-encoded CDRH3 features to interact with a conserved RBD region that overlaps with class 4 bnAb site. Group 2 bnAbs recognize a less well-characterized "site V" on the RBD and destabilize spike trimer. The site V has remained largely unchanged in SARS-CoV-2 variants and is highly conserved across diverse sarbecoviruses, making it a promising target for broad coronavirus vaccine development. Our findings suggest that targeted vaccine strategies may be needed to induce effective B cell responses to escape resistant subdominant spike RBD bnAb sites.

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