ISDA

Entry Detail

PDB ID:

8D48

EMDB ID:

EMD-27177

Keywords:

ANTIVIRAL PROTEIN

Title:

sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2, Homo sapiens

Host Organism:

Homo sapiens

PDB Version:

Deposition Date:

2022-06-01

Release Date:

2023-01-25

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.70 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Chain IDs:A
Chain Length:1259
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)
Description:sd1.040 Fab heavy chain
Chain IDs:B (auth: H)
Chain Length:233
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Description:sd1.040 Fab light chain
Chain IDs:C (auth: L)
Chain Length:220
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

Primary Citation

Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein.

Bianchini, F, Crivelli, V, Abernathy, M.E, Guerra, C, Palus, M, Muri, J, Marcotte, H, Piralla, A, Pedotti, M, De Gasparo, R, Simonelli, L, Matkovic, M, Toscano, C, Biggiogero, M, Calvaruso, V, Svoboda, P, Cervantes Rincon, T, Fava, T, Podesvova, L, Shanbhag, A.A, Celoria, A, Sgrignani, J, Stefanik, M, Honig, V, Pranclova, V, Michalcikova, T, Prochazka, J, Guerrini, G, Mehn, D, Ciabattini, A, Abolhassani, H, Jarrossay, D, Uguccioni, M, Medaglini, D, Pan-Hammarstrom, Q, Calzolai, L, Fernandez, D, Baldanti, F, Franzetti-Pellanda, A, Garzoni, C, Sedlacek, R, Ruzek, D, Varani, L, Cavalli, A, Barnes, C.O, Robbiani, D.F, Bianchini, F, Crivelli, V, Abernathy, M.E, Guerra, C, Palus, M, Muri, J, Marcotte, H, Piralla, A, Pedotti, M, Gasparo, R, Simonelli, L, Matkovic, M, Toscano, C, Biggiogero, M, Calvaruso, V, Svoboda, P, Rincon, T.C, Fava, T, Podesvova, L, Shanbhag, A.A, Celoria, A, Sgrignani, J, Stefanik, M, Honig, V, Pranclova, V, Michalcikova, T, Prochazka, J, Guerrini, G, Mehn, D, Ciabattini, A, Abolhassani, H, Jarrossay, D, Uguccioni, M, Medaglini, D, Pan-Hammarstrom, Q, Calzolai, L, Fernandez, D, Baldanti, F, Franzetti-Pellanda, A, Garzoni, C, Sedlacek, R, Ruzek, D, Varani, L, Cavalli, A, Barnes, C.O, Robbiani, D.F.Show

Sci Immunol 8 eade0958 eade0958 (2023)

PMID: 36701425 DOI: 10.1126/sciimmunol.ade0958

Abstact

Emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike glycoprotein that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera, including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization, and, similar to fp.006 and hr2.016, protects mice expressing human angiotensin-converting enzyme 2 against infection when present as a bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae, including SARS-CoV-2 variants.

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Chemical

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Primary Citation of related structures