ISDA

Deposition Date 2020-07-24

Release Date 2021-01-20

Last Version Date 2024-10-23

Entry Detail

PDB ID:

7CM4

Keywords:

VIRAL PROTEIN

Title:

Crystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59

Biological Source:

Source Organism:

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

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.71 Å

R-Value Free:

0.24

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

I 2 2 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Chain IDs:A
Chain Length:226
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Polymer Type:polypeptide(L)
Molecule:IgG heavy chain
Chain IDs:B (auth: H)
Chain Length:458
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:IgG light chain
Chain IDs:C (auth: L)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

EDO

Primary Citation

A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein.

Kim, C, Ryu, D.K, Lee, J, Kim, Y.I, Seo, J.M, Kim, Y.G, Jeong, J.H, Kim, M, Kim, J.I, Kim, P, Bae, J.S, Shim, E.Y, Lee, M.S, Kim, M.S, Noh, H, Park, G.S, Park, J.S, Son, D, An, Y, Lee, J.N, Kwon, K.S, Lee, J.Y, Lee, H, Yang, J.S, Kim, K.C, Kim, S.S, Woo, H.M, Kim, J.W, Park, M.S, Yu, K.M, Kim, S.M, Kim, E.H, Park, S.J, Jeong, S.T, Yu, C.H, Song, Y, Gu, S.H, Oh, H, Koo, B.S, Hong, J.J, Ryu, C.M, Park, W.B, Oh, M.D, Choi, Y.K, Lee, S.Y.Show

Nat Commun 12 288 288 (2021)

PMID: 33436577 DOI: 10.1038/s41467-020-20602-5

Abstact

Vaccines and therapeutics are urgently needed for the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we screen human monoclonal antibodies (mAb) targeting the receptor binding domain (RBD) of the viral spike protein via antibody library constructed from peripheral blood mononuclear cells of a convalescent patient. The CT-P59 mAb potently neutralizes SARS-CoV-2 isolates including the D614G variant without antibody-dependent enhancement effect. Complex crystal structure of CT-P59 Fab/RBD shows that CT-P59 blocks interaction regions of RBD for angiotensin converting enzyme 2 (ACE2) receptor with an orientation that is notably different from previously reported RBD-targeting mAbs. Furthermore, therapeutic effects of CT-P59 are evaluated in three animal models (ferret, hamster, and rhesus monkey), demonstrating a substantial reduction in viral titer along with alleviation of clinical symptoms. Therefore, CT-P59 may be a promising therapeutic candidate for COVID-19.

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Primary Citation of related structures