REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
Fab | Dejnirattisai et al., 2021 | N/A |
IgG | Dejnirattisai et al., 2021 | N/A |
Human anti-NP (mAb 206) | Dejnirattisai et al., 2021 | N/A |
Regeneron mAbs | AstraZeneca | Cat#REGN10933, and REGN10987 |
AstraZeneca mAbs | AstraZeneca | Cat#AZD1061, AZD8895 |
Vir mAbs | Adagio | Cat#S309 |
Lilly mAbs | Adagio | Cat#Ly-CoV555, and Cat#Ly-CoV16 |
Adagio mAbs | Adagio | Cat#ADG10, Cat#ADG20, and Cat#ADG30 |
Anti-Human IgG (Fc specific)-Peroxidase | Sigma | Cat#A0170; RRID: AB_257868 |
Bacterial and virus strains | ||
SARS-CoV-2 (Australia/VIC01/2020) | Caly et al., 2020 | N/A |
SARS-CoV-2/B.1.1.7 | Public Health England | N/A |
SARS-CoV-2/B.1.351 | Public Health England | N/A |
SARS-CoV-2/P.1 | This paper | N/A |
DH5α bacteria | In Vitrogen | Cat#18263012 |
Biological samples | ||
Serum from Pfizer-vaccinated individuals | University of Oxford | N/A |
Serum from AstraZeneca-Oxford-vaccinated individuals | University of Oxford | N/A |
Plasma from SARS-CoV-2 patients | John Radcliffe Hospital in Oxford UK | N/A |
Chemicals, peptides, and recombinant proteins | ||
His-tagged SARS-CoV-2 RBD | This paper | N/A |
His-tagged SARS-CoV-2 RBD K417N, E484K, N501Y | This paper | N/A |
His-tagged human ACE2 | This paper | N/A |
Human ACE2-hIgG1Fc | This paper | N/A |
Phosphate buffered saline tablets | Sigma-Aldrich | Cat#P4417 |
Dulbecco’s Modified Eagle Medium, high glucose | Sigma-Aldrich | Cat#D5796 |
Dulbecco’s Modified Eagle Medium, low glucose | Sigma-Aldrich | Cat#D6046 |
FreeStyle 293 Expression Medium | GIBCO | Cat#12338018 |
L-Glutamine–Penicillin–Streptomycin solution | Sigma-Aldrich | Cat#G1146 |
GlutaMAX | GIBCO | Cat#35050061 |
UltraDOMA PF Protein-free Medium | Lonza | Cat#12-727F |
Fetal Bovine Serum | GIBCO | Cat#12676029 |
Polyethylenimine, branched | Sigma-Aldrich | Cat#408727 |
Carboxymethyl cellulose | Sigma | Cat#C4888 |
Strep-TactinXT | IBA Lifesciences | Cat#2-1206-025 |
HEPES | Melford | Cat#34587-39108 |
Sodium Chloride | Honeywell | Cat#SZBF3340H |
LB broth | Fisher Scientific UK | Cat#51577-51656 |
Mem Neaa (100X) | GIBCO | Cat#2203945 |
Trypsin-EDTA | GIBCO | Cat#2259288 |
L-Glutamine 200 mM (100X) | GIBCO | Cat#2036885 |
SYPROorange (5000X in DMSO) | Thermo | Cat#S6651 |
Isopropyl β-d-1-thiogalactopyranoside | Meridian Bioscience | Cat#BIO-37036 |
Kanamycin | Melford | Cat#K22000 |
Lysozyme | Sigma-Aldrich | Cat#L6876 |
Tris-base | Melford | Cat#T60040 |
Imidazole | Sigma-Aldrich | Cat#56750 |
Triton X-100 | Sigma-Aldrich | Cat#8787 |
Turbonuclease | Sigma-Aldrich | Cat#T4330 |
RNase A | QIAGEN | Cat#158922 |
NaCl | Sigma-Aldrich | Cat#S9888 |
MgSO4 | Sigma-Aldrich | Cat#746452 |
Na2HPO4 | Melford | Cat#S23100 |
NaH2PO4 | Melford | Cat#S23185 |
Deposited data | ||
The coordinates and structure factors of the SARS-CoV-2 wild type, K417N, K417T, P.1.1.7, P.1.351 and P.1 RBD with 222 and EY6A Fabs, and SARS-CoV-2 P.1 RBD with ACE2 crystallographic complexes | This paper | PDB:7NX6, 7NX7, 7NX8, 7NX9, 7NXA, 7NXB, 7NXC |
Experimental models: cell lines | ||
HEK293S GnTI- cells | ATCC | Cat#CRL-3022; RRID: CVCL_A785 |
HEK293 cells | ATCC | Cat#CRL-3216; RRID: CVCL_0063 |
Expi293F Cells | GIBCO, | Cat#A14527 |
HEK293T cells | ATCC | Cat#CRL-11268 |
Hamster: ExpiCHO cells | Thermo Fisher | Cat#A29133 |
Vero cells | ATCC | Cat#CCL-81; RRID: CVCL_0059 |
Recombinant DNA | ||
Vector: pHLsec | Aricescu et al., 2006 | N/A |
Vector: pNEO | Aricescu et al., 2006 | N/A |
Vector: pOPING-ET | Nettleship et al., 2008 | N/A |
human ACE2 cDNA | Sourcebiosciences | Cat#5297380 |
Vector: human IgG1 heavy chain | German Cancer Research Center, Heidelberg, Germany (H. Wardemann | N/A |
Vector: human lambda light chain | German Cancer Research Center, Heidelberg, Germany (H. Wardemann | N/A |
Vector: human kappa light chain | German Cancer Research Center, Heidelberg, Germany (H. Wardemann | N/A |
Vector: Human Fab | Univeristy of Oxford | N/A |
Vector: Human scFv | University of Oxford, NDM (G. Screaton) | N/A |
Software and algorithms | ||
COOT | Emsley and Cowtan, 2004 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
Xia2-dials | Winter et al., 2018 | https://xia2.github.io/parameters.html |
PHENIX | Liebschner et al., 2019 | https://www.phenix-online.org/ |
PyMOL | DeLano | https://pymol.org/2/; RRID: SCR_000305 |
Data Acquisition Software 11.1.0.11 | Fortebio | https://www.sartorius.com/en/products/protein-analysis/octet-systems-software |
Data Analysis Software HT 11.1.0.25 | Fortebio | https://www.sartorius.com/en/products/protein-analysis/octet-systems-software |
Prism 8.0 | GraphPad | https://www.graphpad.com/scientific-software/prism/; RRID: SCR_002798 |
IBM SPSS Software 26 | IBM | https://www.ibm.com/us-en/?ar=1; RRID: SCR_019096 |
mabscape | This paper |
https://github.com/helenginn/mabscape https://snapcraft.io/mabscape |
Other | ||
X-ray data were collected at beamline I03, Diamond Light Source, under proposal lb27009 for COVID-19 rapid access | This paper | https://www.diamond.ac.uk/covid-19/for-scientists/rapid-access.html |
TALON Superflow Metal Affinity Resin | Clontech | Cat#635668 |
HiLoad 16/600 Superdex 200 pg | Cytiva | Cat#28-9893-35 |
Superdex 200 increase 10/300 GL column | Cytiva | Cat#28990944 |
HisTrap HP 5-ml column | Cytiva | Cat#17524802 |
HiTrap Heparin HT 5-ml column | Cytiva | Cat#17040703 |
Amine Reactive Second-Generation (AR2G) Biosensors | Fortebio | Cat#18-5092 |
Octet RED96e | Fortebio | https://www.sartorius.com/en/products/protein-analysis/octet-label-free-detection-systems |
Buffer exchange system “QuixStand” | GE Healthcare | Cat#56-4107-78 |
Cartesian dispensing system | Genomic solutions | Cat#MIC4000 |
Hydra-96 | Robbins Scientific | Cat#Hydra-96 |
96-well crystallization plate | Greiner bio-one | Cat#E20113NN |
Crystallization Imaging System | Formulatrix | Cat#RI-1000 |
Sonics vibra-cell vcx500 sonicator | VWR | Cat#432-0137 |