ISDA

Deposition Date 2020-06-12

Release Date 2020-06-24

Last Version Date 2024-11-20

Entry Detail

PDB ID:

6ZCZ

Keywords:

VIRAL PROTEIN

Title:

Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody.

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
Lama glama (Taxon ID: 9844)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.65 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

H 3

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:A (auth: E)
Chain Length:205
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Polymer Type:polypeptide(L)
Molecule:Nanobody
Chain IDs:B (auth: F)
Chain Length:151
Number of Molecules:1
Biological Source:Lama glama

Polymer Type:polypeptide(L)
Molecule:EY6A heavy chain
Chain IDs:C (auth: H)
Chain Length:226
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:EY6A light chain
Chain IDs:D (auth: L)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

NAG

Primary Citation

Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.

Zhou, D, Duyvesteyn, H.M.E, Chen, C.P, Huang, C.G, Chen, T.H, Shih, S.R, Lin, Y.C, Cheng, C.Y, Cheng, S.H, Huang, Y.C, Lin, T.Y, Ma, C, Huo, J, Carrique, L, Malinauskas, T, Ruza, R.R, Shah, P.N.M, Tan, T.K, Rijal, P, Donat, R.F, Godwin, K, Buttigieg, K.R, Tree, J.A, Radecke, J, Paterson, N.G, Supasa, P, Mongkolsapaya, J, Screaton, G.R, Carroll, M.W, Gilbert-Jaramillo, J, Knight, M.L, James, W, Owens, R.J, Naismith, J.H, Townsend, A.R, Fry, E.E, Zhao, Y, Ren, J, Stuart, D.I, Huang, K.A.Show

Nat.Struct.Mol.Biol. 27 950 958 (2020)

PMID: 32737466 DOI: 10.1038/s41594-020-0480-y

Abstact

The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (KD of 2 nM), and a 2.6-Å-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19.

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Primary Citation of related structures