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, REGN10987 |
AstraZeneca mAbs |
AstraZeneca |
Cat#AZD1061, AZD8895 |
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 |
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 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 |
Fetal Bovine Serum |
GIBCO |
Cat#12676029 |
Polyethylenimine, branched |
Sigma-Aldrich |
Cat#408727 |
Carboxymethyl cellulose |
Sigma |
Cat#C4888 |
Strep-Tactin®XT |
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 RBD-N501/Fab269 and SARS-CoV-2 RBD-501Y/Fab269 crystallographic complexes |
This paper |
PDB: 7NEH, 7NEG
|
|
Experimental models: cell lines |
|
HEK293S GnTI- cells |
ATCC |
Cat#CRL-3022; RRID:CVCL_A785 |
HEK293 cells |
ATCC |
Cat#CRL-3216 |
Expi293F Cells |
GIBCO, |
Cat#A14527; RRID:CVCL_0063 |
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 |
|
Xia2-dials |
Winter et al., 2018 |
https://xia2.github.io/parameters.html |
PHENIX |
Liebschner et al., 2019 |
https://www.phenix-online.org/ |
COOT |
Emsley and Cowtan, 2004 |
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
PyMOL |
Warren DeLano and Sarina Bromberg |
https://pymol.org/2/ |
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/ |
IBM SPSS Software 26 |
IBM |
https://www.ibm.com/us-en/?ar=1 |
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 mx19946 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 |
Sonics vibra-cell vcx500 sonicator |
VWR |
Cat#432-0137 |
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 |