REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
Emibetuzumab | Jain et al., 2017 | N/A |
Elotuzumab | Jain et al., 2017 | N/A |
Mouse anti-Myc-Tag antibody (9B11) | Cell Signaling Technology | Cat#2276S; RRID: AB_331783 |
Chicken anti-His-Tag antibody | Invitrogen | Cat#PA1-9531; RRID: AB_1069887 |
Goat anti-mouse IgG AlexaFluor 488 | Invitrogen | Cat#A11001; RRID: AB_2534069 |
Donkey anti-chicken IgY F(ab’)2 AlexaFluor 647 | Jackson ImmunoResearch | Cat#703-606-155; RRID: AB_2340380 |
Goat anti-human IgG AlexaFluor 647 | Jackson ImmunoResearch | Cat#109-605-098; RRID: AB_2337889 |
Goat anti-human Fc F(ab’)2 AlexaFluor 488 | Invitrogen | Cat#H10120; RRID: AB_2536548 |
Bacterial and virus strains | ||
DH5α | Julian et al., 2017 | N/A |
SARS-Related Coronavirus 2, Isolate USA-WA1/2020 | BEI | Cat#NR-52281 |
Chemicals, peptides, and recombinant proteins | ||
SARS-CoV-2 (COVID-19) S protein RBD, Fc Tag (RBD-Fc) | Acro Biosystems | Cat#SPD-C5255 |
Biotinylated SARS-CoV-2 (COVID-19) S protein RBD, His, Avitag (bRBD) | Acro Biosystems | Cat#SPD-C82E9 |
Biotinylated SARS-CoV-2 (COVID-19) S1 protein, His, Avitag | Acro Biosystems | Cat#S1N-C82E8 |
SARS-CoV S protein RBD, His Tag | Acro Biosystems | Cat#SPD-S52H6 |
SARS-CoV-2 S protein (R683A, R685A), His Tag, active trimer | Acro Biosystems | Cat#SPN-C52H8 |
Recombinant Human Angiotensin-converting Enzyme 2 (ACE2) | RayBiotech | Cat#230-30165 |
Taq DNA Polymerase with Standard Taq Buffer | New England Biolabs | Cat#M0273L |
8-Oxo-2'-deoxyguanosine-5'-Triphosphate | TriLink Biotechnologies | Cat#N-2034 |
2’-Deoxy-P-nucleoside-5'-Triphosphate | TriLink Biotechnologies | Cat#N-2037 |
Q5 High-Fidelity DNA Polymerase | New England Biolabs | Cat#M0491L |
NheI-HF | New England Biolabs | Cat#R3131L |
HindIII-HF | New England Biolabs | Cat#R3104L |
Quick CIP calf intestinal alkaline phosphatase | New England Biolabs | Cat#M0525L |
T4 ligase | New England Biolabs | Cat#M0202L |
F17 media | Thermo Fisher Scientific | Cat#A1383502 |
Glutamine | Invitrogen | Cat#25030081 |
Kolliphor | Fisher Scientific | Cat#NC0917244 |
G418 | Thermo Fisher Scientific | Cat#10131035 |
Yeastolate | BD Biosciences | Cat#292804 |
Luciferase substrate | Promega ONE-Glo | Cat#E6110 |
Streptavidin AlexaFluor 647 | Invitrogen | Cat#S32357 |
Protein Thermal Shift Dye | Applied Biosystems | Cat#4461146 |
cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail | Sigma Aldrich | Cat#4693159001 |
cOmplete, EDTA-free Protease Inhibitor Cocktail | Sigma Aldrich | Cat#11873580001 |
1% n-dodecyl-b-D-maltopyranoside | Sigma Aldrich | Cat#D4641 |
Sulfo-NHS-LC-biotin | Thermo Fisher Scientific | Cat#21335 |
Critical commercial assays | ||
DC Protein Assay Reagents Package | BioRad | Cat#5000116 |
Deposited data | ||
KA1 | This paper | GenBank: MZ133804 |
KC3 | This paper | GenBank: MZ133805 |
KC1 | This paper | GenBank: MZ133806 |
KA1.ep1 | This paper | GenBank: MZ133807 |
KC3.ep3 | This paper | GenBank: MZ133808 |
KC3.ep5 | This paper | GenBank: MZ133809 |
K7.13 | This paper | GenBank: MZ133810 |
K7.19 | This paper | GenBank: MZ133811 |
Ty1 | Hanke et al., 2020 | PDB: 6ZXN |
VHH-72 | Wrapp et al., 2020 | PDB: 6WAQ |
CB6 | Shi et al., 2020 | PDB: 7C01 |
C119 |
Barnes et al., 2020 Provided by laboratories of Pamela Bjorkman (California Institute of Technology) and Michel Nussenzweig (The Rockefeller University) |
PDB: 7K8W |
S309 |
Pinto et al., 2020 Provided by laboratories of Pamela (California Institute of Technology) Bjorkman and Michel Nussenzweig (The Rockefeller University) |
PDB: 6WPS |
CR3022 | Yuan et al. | PDB: 6W41 |
Experimental models: Cell lines | ||
Human: HEK293-6E | National Research Council (NRC) of Canada | N/A |
Human: Lenti-X 293T | Takara | Cat#632180 |
Human: 293T-ACE2 | BEI | Cat#NR-52511 |
Cercopithecus aethiops: VeroE6 | ATCC | Cat#CRL1586 |
Hamster: CHO | Gibco | Cat#A29133 |
Yeast: EBY100 | Julian et al. 2017 | N/A |
Recombinant DNA | ||
HDM-Hgpm2 plasmid encoding HIV Gag-Pol under CMV promoter | BEI | Cat#NR-52517 |
HDM-tat1b plasmid encoding HIV Tat under CMV promoter | BEI | Cat#NR-52518 |
pRC14 CMV-Rev1b plasmid encoding HIV Rev | BEI | Cat#NR-52519 |
pHAGE-CMV-Luc2-IRES-ZsGreen-W lentiviral transfer plasmid encoding co-expression of luciferase and ZsGreen | BEI | Cat#NR-52516 |
pCMV3 SARS-CoV2 S Untagged Delta 19AA C-term plasmid encoding the SARS-CoV-2 spike (S) protein with a 19-amino acid deletion at the C-terminus | Provided by the laboratory of Marilia Cascalho (University of Michigan) | N/A |
Software and algorithms | ||
Python version 3.7 | Python Software Foundation | https://www.python.org |
Code for curve fitting | This paper | https://GitHub.com/mduncans/Data_Fitting |
Others | ||
Synthetic nanobody library |
McMahon et al., 2018 Provided by the laboratory of Andrew Kruse (Harvard Medical School) |
N/A |
Streptavidin MicroBeads | Miltenyi Biotec | Cat#130-048-101 |
Zymoprep Yeast Plasmid Miniprep II | Zymo Research | Cat#D2004 |
Streptavidin Dynabeads | Invitrogen | Cat#11047 |
Protein A magnetic beads | Invitrogen | Cat#88846 |
QIAquick Gel Extraction Kit | Qiagen | Cat#28704 |
QIAquick PCR Purification Kit | Qiagen | Cat#28104 |
QIAprep Spin Miniprep Kit | Qiagen | Cat#27106 |
Protein A Agarose | Thermo Fisher Scientific | Cat#20333 |
Centrifuge columns | Thermo Fisher Scientific | Cat#89898 |
Zeba Spin Desalting Columns | Thermo Fisher Scientific | Cat#89894; Cat#89892; Cat#89890 |
Invitrogen NuPAGE 10% Bis-Tris, 1.0 mm, Midi Protein GEL (SDS-PAGE) | Thermo Fisher Scientific | Cat#WG1203BOX |
Lenti-X Concentrator | Takara | Cat#631232 |
Superdex 200 Increase 10/300 GL column | GE | Cat#28990944 |
96-well plates | VWR | Cat#650261 |