ISDA

Entry Detail

PDB ID:

8SDF

Keywords:

IMMUNE SYSTEM

Title:

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.4

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2, Homo sapiens

Host Organism:

Trichoplusia ni

PDB Version:

Deposition Date:

2023-04-06

Release Date:

2024-03-13

Method Details:

Experimental Method:

X-RAY DIFFRACTION

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

Download Validation Report

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

Protein Blast

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

UniProt ID:P0DTC2 Pfam ID:PF09408

Ligand Molecules

MPD

NAG

Primary Citation

Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.

Song, G, Yuan, M, Liu, H, Capozzola, T, Lin, R.N, Torres, J.L, He, W.T, Musharrafieh, R, Dueker, K, Zhou, P, Callaghan, S, Mishra, N, Yong, P, Anzanello, F, Avillion, G, Vo, A.L, Li, X, Makhdoomi, M, Feng, Z, Zhu, X, Peng, L, Nemazee, D, Safonova, Y, Briney, B, Ward, A.B, Burton, D.R, Wilson, I.A, Andrabi, R.Show

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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Primary Citation of related structures