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TitleNeutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2.
Journal, issue, pagesNat Struct Mol Biol, Vol. 27, Issue 9, Page 846-854, Year 2020
Publish dateJul 13, 2020
AuthorsJiandong Huo / Audrey Le Bas / Reinis R Ruza / Helen M E Duyvesteyn / Halina Mikolajek / Tomas Malinauskas / Tiong Kit Tan / Pramila Rijal / Maud Dumoux / Philip N Ward / Jingshan Ren / Daming Zhou / Peter J Harrison / Miriam Weckener / Daniel K Clare / Vinod K Vogirala / Julika Radecke / Lucile Moynié / Yuguang Zhao / Javier Gilbert-Jaramillo / Michael L Knight / Julia A Tree / Karen R Buttigieg / Naomi Coombes / Michael J Elmore / Miles W Carroll / Loic Carrique / Pranav N M Shah / William James / Alain R Townsend / David I Stuart / Raymond J Owens / James H Naismith /
PubMed AbstractThe SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than influenza. The SARS-CoV-2 receptor binding domain (RBD) of the spike protein binds to the ...The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than influenza. The SARS-CoV-2 receptor binding domain (RBD) of the spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor as a prelude to viral entry into the cell. Using a naive llama single-domain antibody library and PCR-based maturation, we have produced two closely related nanobodies, H11-D4 and H11-H4, that bind RBD (K of 39 and 12 nM, respectively) and block its interaction with ACE2. Single-particle cryo-EM revealed that both nanobodies bind to all three RBDs in the spike trimer. Crystal structures of each nanobody-RBD complex revealed how both nanobodies recognize the same epitope, which partly overlaps with the ACE2 binding surface, explaining the blocking of the RBD-ACE2 interaction. Nanobody-Fc fusions showed neutralizing activity against SARS-CoV-2 (4-6 nM for H11-H4, 18 nM for H11-D4) and additive neutralization with the SARS-CoV-1/2 antibody CR3022.
External linksNat Struct Mol Biol / PubMed:32661423
MethodsEM (single particle) / X-ray diffraction
Resolution3.3 - 3.7 Å
Structure data

11068

6z43

EMDB-11068, PDB-6z43:
Cryo-EM Structure of SARS-CoV-2 Spike : H11-D4 Nanobody Complex
Method: EM (single particle) / Resolution: 3.3 Å

11218

6zhd

EMDB-11218, PDB-6zhd:
H11-H4 bound to Spike
Method: EM (single particle) / Resolution: 3.7 Å

PDB-6zh9:
Ternary complex CR3022 H11-H4 and RBD (SARS-CoV-2)
Method: X-RAY DIFFRACTION / Resolution: 3.31 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • lama glama (llama)
  • enterobacteria phage t4 (virus)
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / Spike / nanobody / VHH / SARS-CoV-2 / COVID-19 / ANTIVIRAL PROTEIN / Covid19 / llama / neutralisation

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