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. 2023 Mar 31;26(4):106540. doi: 10.1016/j.isci.2023.106540
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
COVA1-18 Isolated from patient (Brouwer et al.8) N/A
COVA2-02 Isolated from patient (Brouwer et al.8) N/A
COVA2-15 Isolated from patient (Brouwer et al.8) N/A
COVA1-16 Isolated from patient (Brouwer et al.8) N/A
HC84.26 Keck et al.55 N/A
COVA1-18/2-15 bispecific antibody This study N/A
COVA1-16/2-15 bispecific antibody This study N/A
COVA1-16/2-02 bispecific antibody This study N/A
COVA2-02/2-15 bispecific antibody This study N/A
COVA1-16/HC84.26 bispecific antibody This study N/A
COVA1-18/HC84.26 bispecific antibody This study N/A
COVA2-02/HC84.26 bispecific antibody This study N/A
COVA2-15/HC84.26 bispecific antibody This study N/A
goat anti-Human IgG κ Bethyl Laboratories Cat# A80-126A
goat anti-Human IgG λ Bethyl Laboratories Cat# A80-116
2G12-IgG1 Trkola et al. 199669 N/A
Bacterial and virus strains
SARS-CoV-2 virus German isolate; GISAID ID EPI_ISL 406862 European Virus Archive Global #026V-03883
SARS-CoV-2 Beta hCoV-19/Netherlands/NH-RIVM-20432/2020_p2 European Virus Archive Global # 014V-04031
SARS-CoV-2 Gamma hCoV-19/Netherlands/NoordHolland-10159/2021_p2 European Virus Archive Global # 014V-04058
Chemicals, peptides, and recombinant proteins
Prefusion SARS-CoV-2 S Described in Brouwer et al.8 N/A
Prefusion SARS-CoV-2 Beta Described in Caniels et al.49 N/A
Prefusion SARS-CoV S Described in Pallesen et al.70 N/A
SARS-CoV-2-6P-Mut7 Described in Torres et al.71 N/A
RBD of the SARS-CoV-2 S Described in Brouwer et al.8 N/A
RBD of the SARS-CoV S protein Described in Brouwer et al.8 N/A
PBS Thermo Fisher Cat# 10010023
PEI MAX Polysciences Cat# 24765-1
2-mercaptoethylamine (2-MEA) Sigma Cat# M9768-25G
Casein buffer Thermo Scientific Cat# 37528
Lipofectamine 2000 Life Technologies Cat# 11668-019
Penicillin Sigma-Aldrich Cat# P3032-10MI
Streptomycin VWR Cat# 382-EU-100G
3,3’,5,5’-tetranethylbenzidine Sigma-Aldrich Cat# T4444
Sodium acetate Sigma-Aldrich Cat# 127-09-3
Hydrogen peroxide Thermo Fisher Cat# H/1750/17
Citric acid Sigma-Aldrich Cat# 77-92-9
Sodium bicarbonate Fisher Scientific Cat# 144-55-8
2% (w/v) uranyl-formate Electron Microscopy Sciences Cat # 22451
PKH26 dye Sigma-Aldrich Cat# PKH26GL
Carboxyfluorescein succinimidyl ester Thermofisher Cat# C34554
IgG4Δhinge-L368A Rose et al.72 N/A
IgG1-Campath Genmab N/A
Equine spleen apoferritin Sigma-Aldrich A3660
GroEL Van Duijn et al. 200573 N/A
Tris Sigma-Aldrich T7943
Critical commercial assays
Quickchange site-directed mutagenesis kit NEB Cat# E0554S
Nano-Glo Luciferase Assay System Promega Cat# N1130
Experimental models: Cell lines
FreeStyle 293F cells Thermo Fisher Cat# R79007
HEK 293T/ACE2 cells Schmidt et al. 202074 N/A
HEK 293T cells ATCC Cat# CRL-11268
THP-1 cells ATCC ATCC® TIB-202
VeroE6 ATCC ATCC® CRL 1586TM
Recombinant DNA
SARS-CoV-2-SΔ19 plasmid Schmidt et al. 202074 N/A
SARS-CoV-2 S pPPI4 plasmid Brouwer et al.8 N/A
SARS-CoV-2 RBD pPPI4 plasmid Brouwer et al.8 N/A
gblock HC84.26 Genscript N/A
SARS-CoV-2 D614G S Brouwer et al.8 N/A
SARS-CoV-2 Alpha S Described in Caniels et al.49 N/A
SARS-CoV-2 Beta S Described in Caniels et al.49 N/A
SARS-CoV-2 Gamma S Described in Caniels et al.49 N/A
SARS-CoV-2 Delta S Described in Caniels et al.49 N/A
SARS-CoV-2 Omicron BA.1 S Described in Caniels et al.49 N/A
SARS-CoV-2 BA.2 S Described in Caniels et al.49 N/A
SARS-CoV-2 BA.4/5 S Described in Caniels et al.49 N/A
E2-His Genscript Biotech Genbank: ABN11232.1, AF009606.1
pHIV-1NL43ΔENV-NanoLuc plasmid Schmidt et al., 202074 N/A
Software and algorithms
GraphPad Prism v8.3.0 GraphPad N/A
UCSF Chimera Pettersen et al.75 N/A
UCSF ChimeraX Pettersen et al.76 N/A
Leginon Potter et al.77 N/A
Appion Lander et al.78 N/A
DoG-picker Voss et al.79 N/A
RELION 3.0 Scheres80 N/A
DiscoverMP Refeyn N/A
SciPy 1.5 Virtanen et al.81 https://scipy.org
AcquireMP Refeyn N/A
Python version 3.9 Python Software Foundation https://www.python.org
Other
Vivaspin 500, 3 kDa MWCO, Polyethersulfone Sigma-Aldrich Cat# GE28-9322-18
Vivaspin 20, 100.000 kDa MWCO, Polyethersulfone Sigma-Aldrich Cat# GE28-9323-63
Ni-NTA agarose QIAGEN Cat# 30210
Ni-NTA HighSorb plates QIAGEN Cat# 35061
Superose 6 increase 10/300 GL Sigma-Aldrich Cat# GE29-0915-96
Octet K2 system Sartorius (FortéBio) N/A
Octet Biosensors: Protein A Sartorius (FortéBio) Cat# 18-5010
Octet Biosensors: NiNTA Sartorius (FortéBio) Cat# 18-5101
Nucleobond Xtra Maxi kit Macherey-Nagel Cat# 740414.50
Fast Digest BshTI Thermo Scientific Cat# FD1464
Fast Digest XhoI Thermo Scientific Cat# FD0694
Fast Digest Green buffer 10x Thermo Scientific Cat# B72
Streptavidin-PE Thermo Fisher Scientific Cat# 12-4317-87
FreeStyle 293 Expression medium Thermo Scientific Cat# 12338018
DMEM Sigma-Aldrich Cat# D6429-500ML
Glutamax supplement Thermo Fisher Cat# 35050061
High-binding plates: Half-area 96-well polystyrene high-binding microplate Greiner Cat# 675061
Steritop Filter Units Merckmillipore Cat# C3239
Glomax Turner BioSystems Model# 9101-002
Microplate 96 well half area white Greiner bio-one Cat# 675074
Hepes (1M, GIBCO) Thermofisher scientific Cat# 15630106
Greiner CELLSTAR® 96 well plates round bottom clear wells Merck Cat# M9436
MEM Non-Essential Amino Acids Solution Thermo Fisher Cat# 11140050
Greiner CELLSTAR 96 well plates round bottom clear wells Merck Cat# M9436
Protein G Agarose Thermo Scientific Pierce Cat# 10016363
NanoDrop One Thermofisher Cat# ND-ONE-W
Spectrophotometer BMG Labtech N/A
Carbon-coated 400-mesh copper grids Electron Microscopy Sciences Cat # 0400-Cu
Tecnai T12 Spirit FEI Company N/A
4kx4k Eagle CCD camera FEI Company N/A
0.22 μm PVDF syringe filter Merck Cat# GVWP02500
Lipofectamine Thermofisher Cat# 18324012
Flow Cytometry System BD FACSCanto II N/A
Fluorescent Neutravidin beads Invitrogen Cat# F8776