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. 2021 Jun 24;28(9):1379–1388.e7. doi: 10.1016/j.chembiol.2021.05.019
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