7OLZ

Crystal structure of the SARS-CoV-2 RBD with neutralizing-VHHs Re5D06 and Re9F06

Summary for 7OLZ

• Entry DOI: 10.2210/pdb7olz/pdb
• Descriptor: Nanobody Re5D06, Nanobody Re9F06, Spike protein S1, ... (6 entities in total)
• Functional Keywords: covid19, neutralizing vhh, viral protein
• Biological source: Vicugna pacos; More
• Total number of polymer chains: 3
• Total formula weight: 50448.86

Authors

Aksu, M.,Guttler, T.,Gorlich, D. (deposition date: 2021-05-20, release date: 2021-08-11, Last modification date: 2024-10-16)

Primary citation

Guttler, T.,Aksu, M.,Dickmanns, A.,Stegmann, K.M.,Gregor, K.,Rees, R.,Taxer, W.,Rymarenko, O.,Schunemann, J.,Dienemann, C.,Gunkel, P.,Mussil, B.,Krull, J.,Teichmann, U.,Gross, U.,Cordes, V.C.,Dobbelstein, M.,Gorlich, D.
Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies.
Embo J., 40:e107985-e107985, 2021

PubMed Abstract: Monoclonal anti-SARS-CoV-2 immunoglobulins represent a treatment option for COVID-19. However, their production in mammalian cells is not scalable to meet the global demand. Single-domain (VHH) antibodies (also called nanobodies) provide an alternative suitable for microbial production. Using alpaca immune libraries against the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein, we isolated 45 infection-blocking VHH antibodies. These include nanobodies that can withstand 95°C. The most effective VHH antibody neutralizes SARS-CoV-2 at 17-50 pM concentration (0.2-0.7 µg per liter), binds the open and closed states of the Spike, and shows a tight RBD interaction in the X-ray and cryo-EM structures. The best VHH trimers neutralize even at 40 ng per liter. We constructed nanobody tandems and identified nanobody monomers that tolerate the K417N/T, E484K, N501Y, and L452R immune-escape mutations found in the Alpha, Beta, Gamma, Epsilon, Iota, and Delta/Kappa lineages. We also demonstrate neutralization of the Beta strain at low-picomolar VHH concentrations. We further discovered VHH antibodies that enforce native folding of the RBD in the E. coli cytosol, where its folding normally fails. Such "fold-promoting" nanobodies may allow for simplified production of vaccines and their adaptation to viral escape-mutations.

PubMed: 34302370
DOI: 10.15252/embj.2021107985

Experimental method

X-RAY DIFFRACTION (1.75 Å)