ISDA

Entry Detail

PDB ID:

8Q7S

Keywords:

ANTIVIRAL PROTEIN

Title:

Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2, Vicugna pacos

Host Organism:

Komagataella pastoris

PDB Version:

Deposition Date:

2023-08-16

Release Date:

2023-12-20

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.70 Å

R-Value Free:

0.28

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:A, D, G, J, M
Chain Length:196
Number of Molecules:5
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Polymer Type:polypeptide(L)
Description:VHH Antibody Re21H01
Chain IDs:B, E, H, K, N
Chain Length:117
Number of Molecules:5
Biological Source:Vicugna pacos

Polymer Type:polypeptide(L)
Description:VHH Antibody Ma6F06
Chain IDs:C, F, I, L, O
Chain Length:131
Number of Molecules:5
Biological Source:Vicugna pacos

Ligand Molecules

EDO

GOL

P4G

Primary Citation

Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.

Aksu, M, Kumar, P, Guttler, T, Taxer, W, Gregor, K, Mussil, B, Rymarenko, O, Stegmann, K.M, Dickmanns, A, Gerber, S, Reineking, W, Schulz, C, Henneck, T, Mohamed, A, Pohlmann, G, Ramazanoglu, M, Mese, K, Gross, U, Ben-Yedidia, T, Ovadia, O, Fischer, D.W, Kamensky, M, Reichman, A, Baumgartner, W, von Kockritz-Blickwede, M, Dobbelstein, M, Gorlich, D, Liebschner, D, Afonine, P.V, Baker, M.L, Bunkoczi, G, Chen, V.B, Croll, T.I, Hintze, B, Hung, L.W, Jain, S, McCoy, A.J, Moriarty, N.W, Oeffner, R.D, Poon, B.K, Prisant, M.G, Read, R.J, Richardson, J.S, Richardson, D.C, Sammito, M.D, Sobolev, O.V, Stockwell, D.H, Terwilliger, T.C, Urzhumtsev, A.G, Videau, L.L, Williams, C.J, Adams, P.D, Afonine, P.V, Grosse-Kunstleve, R.W, Echols, N, Headd, J.J, Moriarty, N.W, Mustyakimov, M, Terwilliger, T.C, Urzhumtsev, A, Zwart, P.H, Adams, P.D, Kabsch, W, McCoy, A.J, Emsley, P, Lohkamp, B, Scott, W.G, Cowtan, K.Show

Antiviral Res. 221 105778 105778 (2023)

PMID: 38065245 DOI: 10.1016/j.antiviral.2023.105778

Abstact

The ongoing threat of COVID-19 has highlighted the need for effective prophylaxis and convenient therapies, especially for outpatient settings. We have previously developed highly potent single-domain (VHH) antibodies, also known as nanobodies, that target the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein and neutralize the Wuhan strain of the virus. In this study, we present a new generation of anti-RBD nanobodies with superior properties. The primary representative of this group, Re32D03, neutralizes Alpha to Delta as well as Omicron BA.2.75; other members neutralize, in addition, Omicron BA.1, BA.2, BA.4/5, and XBB.1. Crystal structures of RBD-nanobody complexes reveal how ACE2-binding is blocked and also explain the nanobodies' tolerance to immune escape mutations. Through the cryo-EM structure of the Ma16B06-BA.1 Spike complex, we demonstrated how a single nanobody molecule can neutralize a trimeric spike. We also describe a method for large-scale production of these nanobodies in Pichia pastoris, and for formulating them into aerosols. Exposing hamsters to these aerosols, before or even 24 h after infection with SARS-CoV-2, significantly reduced virus load, weight loss and pathogenicity. These results show the potential of aerosolized nanobodies for prophylaxis and therapy of coronavirus infections.

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