ISDA

Deposition Date 2022-06-28

Release Date 2022-08-24

Last Version Date 2024-10-09

Entry Detail

PDB ID:

8DI5

Keywords:

VIRAL PROTEIN/IMMUNE SYSTEM

Title:

Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with VH domain F6 (focused refinement of RBD and VH F6)

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.04 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Mutations:R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P
Chain IDs:A (auth: C)
Chain Length:1288
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF16451, PF09408, PF19209, PF01601

Polymer Type:polypeptide(L)
Molecule:VH F6
Chain IDs:B (auth: H)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

NAG

Primary Citation

Potent and broad neutralization of SARS-CoV-2 variants of concern (VOCs) including omicron sub-lineages BA.1 and BA.2 by biparatopic human VH domains.

Chen, C, Saville, J.W, Marti, M.M, Schafer, A, Cheng, M.H, Mannar, D, Zhu, X, Berezuk, A.M, Banerjee, A, Sobolewski, M.D, Kim, A, Treat, B.R, Da Silva Castanha, P.M, Enick, N, McCormick, K.D, Liu, X, Adams, C, Hines, M.G, Sun, Z, Chen, W, Jacobs, J.L, Barratt-Boyes, S.M, Mellors, J.W, Baric, R.S, Bahar, I, Dimitrov, D.S, Subramaniam, S, Martinez, D.R, Li, W.Show

Iscience 25 104798 104798 (2022)

PMID: 35875685 DOI: 10.1016/j.isci.2022.104798

Abstact

The emergence of SARS-CoV-2 variants of concern (VOCs) requires the development of next-generation biologics with high neutralization breadth. Here, we characterized a human VH domain, F6, which we generated by sequentially panning large phage-displayed VH libraries against receptor binding domains (RBDs) containing VOC mutations. Cryo-EM analyses reveal that F6 has a unique binding mode that spans a broad surface of the RBD and involves the antibody framework region. Attachment of an Fc region to a fusion of F6 and ab8, a previously characterized VH domain, resulted in a construct (F6-ab8-Fc) that broadly and potently neutralized VOCs including Omicron. Additionally, prophylactic treatment using F6-ab8-Fc reduced live Beta (B.1.351) variant viral titers in the lungs of a mouse model. Our results provide a new potential therapeutic against SARS-CoV-2 variants including Omicron and highlight a vulnerable epitope within the spike that may be exploited to achieve broad protection against circulating variants.

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Primary Citation of related structures