Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

Custodio T, Das H, Sheward D, Hanke L, Pazicky S, Pieprzyk J, Sorgenfrei M, Schroer M, Gruzinov A, Jeffries C, Graewert M, Svergun D, Dobrev N, Remans K, Seeger M, McInerney G, Murrell B, Hällberg B, Löw C
(2020 Jun 23)

doi: 10.1101/2020.06.23.165415
Submitted to SASBDB: 2020 Jun 22
Published in SASBDB:

SASDJF4 – Synthetic nanobody Sybody 23 (Sy23)

Synthetic nanobody Sybody 23 experimental SAS data
CORAL model
Sample: Synthetic nanobody Sybody 23 monomer, 16 kDa synthetic construct protein
Buffer: 50 mM Tris 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 May 5
RgGuinier 2.1 nm
Dmax 8.0 nm
VolumePorod 22 nm3

SASDJG4 – SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD)

Spike glycoprotein (ACE2 receptor binding domain) experimental SAS data
SASREF model
Sample: Spike glycoprotein (ACE2 receptor binding domain) monomer, 29 kDa Severe acute respiratory … protein
Buffer: 25 mM Tris 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 May 1
RgGuinier 3.0 nm
Dmax 13.1 nm
VolumePorod 64 nm3

SASDJH4 – SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23)

Synthetic nanobody Sybody 23Spike glycoprotein (ACE2 receptor binding domain) experimental SAS data
CORAL model
Sample: Synthetic nanobody Sybody 23 monomer, 16 kDa synthetic construct protein
Spike glycoprotein (ACE2 receptor binding domain) monomer, 29 kDa Severe acute respiratory … protein
Buffer: 25 mM Tris 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 May 10
RgGuinier 3.5 nm
Dmax 15.1 nm
VolumePorod 87 nm3