ISDA

Deposition Date 2021-12-23

Release Date 2022-01-19

Last Version Date 2024-11-20

Entry Detail

PDB ID:

7QNX

Keywords:

VIRAL PROTEIN

Title:

The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with Beta-55 and EY6A Fabs

Biological Source:

Source Organism:

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

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.92 Å

R-Value Free:

0.26

R-Value Work:

0.22

R-Value Observed:

0.23

Space Group:

P 32 2 1

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:Beta-55 heavy chain
Chain IDs:C (auth: A)
Chain Length:232
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Beta-55 light chain
Chain IDs:D (auth: B)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Surface glycoprotein
Chain IDs:E
Chain Length:202
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

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

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

Ligand Molecules

Primary Citation

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

Dejnirattisai, W, Huo, J, Zhou, D, Zahradnik, J, Supasa, P, Liu, C, Duyvesteyn, H.M.E, Ginn, H.M, Mentzer, A.J, Tuekprakhon, A, Nutalai, R, Wang, B, Dijokaite, A, Khan, S, Avinoam, O, Bahar, M, Skelly, D, Adele, S, Johnson, S.A, Amini, A, Ritter, T.G, Mason, C, Dold, C, Pan, D, Assadi, S, Bellass, A, Omo-Dare, N, Koeckerling, D, Flaxman, A, Jenkin, D, Aley, P.K, Voysey, M, Costa Clemens, S.A, Naveca, F.G, Nascimento, V, Nascimento, F, Fernandes da Costa, C, Resende, P.C, Pauvolid-Correa, A, Siqueira, M.M, Baillie, V, Serafin, N, Kwatra, G, Da Silva, K, Madhi, S.A, Nunes, M.C, Malik, T, Openshaw, P.J.M, Baillie, J.K, Semple, M.G, Townsend, A.R, Huang, K.A, Tan, T.K, Carroll, M.W, Klenerman, P, Barnes, E, Dunachie, S.J, Constantinides, B, Webster, H, Crook, D, Pollard, A.J, Lambe, T, Paterson, N.G, Williams, M.A, Hall, D.R, Fry, E.E, Mongkolsapaya, J, Ren, J, Schreiber, G, Stuart, D.I, Screaton, G.R, Dejnirattisai, W, Huo, J, Zhou, D, Zahradnik, J, Supasa, P, Liu, C, Duyvesteyn, H.M.E, Ginn, H.M, Mentzer, A.J, Tuekprakhon, A, Nutalai, R, Wang, B, Dijokaite, A, Khan, S, Avinoam, O, Bahar, M, Skelly, D, Adele, S, Johnson, S.A, Amini, A, Ritter, T, Mason, C, Dold, C, Pan, D, Assadi, S, Bellass, A, Omo-Dare, N, Koeckerling, D, Flaxman, A, Jenkin, D, Aley, P.K, Voysey, M, Costa Clemens, S.A, Naveca, F.G, Nascimento, V, Nascimento, F, Fernandes da Costa, C, Resende, P.C, Pauvolid-Correa, A, Siqueira, M.M, Baillie, V, Serafin, N, Ditse, Z, Silva, K.D, Madhi, S, Nunes, M.C, Malik, T, Openshaw, P.J, Baillie, J.K, Semple, M.G, Townsend, A.R, Huang, K.A, Tan, T.K, Carroll, M.W, Klenerman, P, Barnes, E, Dunachie, S.J, Constantinides, B, Webster, H, Crook, D, Pollard, A.J, Lambe, T, Paterson, N.G, Williams, M.A, Hall, D.R, Fry, E.E, Mongkolsapaya, J, Ren, J, Schreiber, G, Stuart, D.I, Screaton, G.R, Dejnirattisai, W, Huo, J, Zhou, D, Zahradnik, J, Supasa, P, Liu, C, Duyvesteyn, H.M.E, Ginn, H.M, Mentzer, A.J, Tuekprakhon, A, Nutalai, R, Wang, B, Dijokaite, A, Khan, S, Avinoam, O, Bahar, M, Skelly, D, Adele, S, Johnson, S.A, Amini, A, Ritter, T, Mason, C, Dold, C, Pan, D, Assadi, S, Bellass, A, Omo-Dare, N, Koeckerling, D, Flaxman, A, Jenkin, D, Aley, P.K, Voysey, M, Costa Clemens, S.A, Naveca, F.G, Nascimento, V, Nascimento, F, Fernandes da Costa, C, Resende, P.C, Pauvolid-Correa, A, Siqueira, M.M, Baillie, V, Serafin, N, Ditse, Z, Silva, K.D, Madhi, S, Nunes, M.C, Malik, T, Openshaw, P.J, Baillie, J.K, Semple, M.G, Townsend, A.R, Huang, K.A, Tan, T.K, Carroll, M.W, Klenerman, P, Barnes, E, Dunachie, S.J, Constantinides, B, Webster, H, Crook, D, Pollard, A.J, Lambe, T, Paterson, N.G, Williams, M.A, Hall, D.R, Fry, E.E, Mongkolsapaya, J, Ren, J, Schreiber, G, Stuart, D.I, Screaton, G.R, Dejnirattisai, W, Huo, J, Zhou, D, Zahradnik, J, Supasa, P, Liu, C, Duyvesteyn, H.M, Ginn, H.M, Mentzer, A.J, Tuekprakhon, A, Nutalai, R, Wang, B, Dijokaite, A, Khan, S, Avinoam, O, Bahar, M, Skelly, D, Adele, S, Johnson, S.A, Amini, A, Ritter, T, Mason, C, Dold, C, Pan, D, Assadi, S, Bellass, A, Omo-Dare, N, Koeckerling, D, Flaxman, A, Jenkin, D, Aley, P.K, Voysey, M, Naveca, F.G, Nascimento, V, Nascimento, F, Resende, P.C, Pauvolid-Correa, A, Siqueira, M.M, Baillie, V, Serafin, N, Kwatra, G, Madhi, S.A, Nunes, M.C, Malik, T, Openshaw, P.J, Baillie, J.K, Semple, M.G, Townsend, A.R, Huang, K.Y.A, Tan, T.K, Carroll, M.W, Klenerman, P, Barnes, E, Dunachie, S.J, Constantinides, B, Webster, H, Crook, D, Pollard, A.J, Lambe, T, Paterson, N.G, Williams, M.A, Hall, D.R, Fry, E.E, Mongkolsapaya, J, Ren, J, Schreiber, G, Stuart, D.I, Screaton, G.R.Show

Cell 185 467 484.e15 (2022)

PMID: 35081335 DOI: 10.1016/j.cell.2021.12.046

Abstact

On 24th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.

Legend

Protein

Chemical

Disease

Primary Citation of related structures