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. 2023 May 22;42(6):112532. doi: 10.1016/j.celrep.2023.112532
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
P2C-1F11 Ge et al.35 PDB code 7CDI
BD-368-2 Du et al.50 PDB code 7CHH
S309 Pinto et al.37 PDB code 6WPS
EY6A Zhou et al.39 PDB code 6ZCZ
VRC01 Zhou et al.51 PDB code 4LST; RRID: AB_2491019
Bacterial and virus strains
E. coli DH5a Takara Cat# 9057
SARS-CoV-2 pseudovirus/wild-type (WT) Ju et al.18 N/A
SARS-CoV-2 pseudovirus/Beta Ju et al.18 N/A
SARS-CoV-2 pseudovirus/Delta Ju et al.18 N/A
SARS-CoV-2 pseudovirus/Omicron BA.1 Ju et al.18 N/A
SARS-CoV-2 pseudovirus/Omicron BA.1.1 This paper N/A
SARS-CoV-2 pseudovirus/Omicron BA.2 Guo et al.52 N/A
SARS-CoV-2 pseudovirus/Omicron BA.2.12.1 Guo et al.52 N/A
SARS-CoV-2 pseudovirus/Omicron BA.4/5 Guo et al.52 N/A
SARS-CoV-2 pseudovirus/Omicron BA.2.75 Guo et al.52 N/A
SARS-CoV-2 pseudovirus/Omicron BQ.1.1 This paper N/A
SARS-CoV-2 pseudovirus/Omicron XBB.1 This paper N/A
Chemicals, peptides, and recombinant proteins
Dulbecco’s Modified Eagle Medium Gibco Cat# 11965–092
Fetal bovine serum Gibco Cat# 10099–141C
Penicillin-Streptomycin (10,000 U/mL) Gibco Cat# 15140163
HEPES (1M) Buffer Solution Gibco Cat# 15630–080
Opti-MEM Reduced Serum Medium Gibco Cat# 51985034
FreeStyle 293 expression medium Gibco Cat# 12338026
Polyethylenimines (PEIs) 25K PolySciences Cat# 23966
Ampicillin Amresco Cat# 69-52-3
DEAE-Dextran hydrochloride Sigma Aldrich Cat# D9885-10G
Acetate 4.5 Cytiva Cat# BR100350
Acetate 5.0 Cytiva Cat# BR100351
HBS-EP+ Buffer 10× Cytiva Cat# BR100669
Glycine 1.5 Cytiva Cat# BR100354
Glycine 2.0 Cytiva Cat# BR100355
BeyoGold His-tag Purification Resin Beyotime Cat# P2233-100mL
Imidazole Sangon Biotech Cat# B540146-0100
L-Cysteine hydrochloride anhydrous Sigma-Aldrich Cat# 30120-50G
Papain from papaya latex lyophilized powder Sigma-Aldrich Cat# P4762-1G
Iodoacetamide Sigma-Aldrich Cat# I6125-25G
0.5 M EDTA, pH 8.0 Invitrogen Cat# 15575-038
SARS-CoV-2 WT RBD probe Sino Biological Inc. Cat# 40592-V08B
Human ACE2 Sino Biological Inc. Cat# 10108-H08H
SARS-CoV-2 BA.2 spike trimer Sino Biological Inc. Cat# 40589-V08H28
SARS-CoV-2 WT RBD with His tag Ju et al.18 N/A
SARS-CoV-2 mutated RBD_N460K with His tag This paper N/A
SARS-CoV-2 mutated RBD_F486V with His tag This paper N/A
SARS-CoV-2 mutated RBD_F486S with His tag This paper N/A
SARS-CoV-2 mutated RBD_N460K + F486V with His tag This paper N/A
SARS-CoV-2 mutated RBD_N460K + F486S with His tag This paper N/A
Critical commercial assays
Bright-Lite Luciferase Assay System Vazyme Biotech Cat# DD1204-03
Gold Hi EndoFree Plasmid Maxi Kit CWBIO Cat# CW2104M
TMB substrate Sangon Biotech Cat# E661007-0100
Mut Express II Fast Mutagenesis Kit V2 Vazyme Biotech Cat# C214-01
HRP Conjugation Kit Abcam Cat# ab102890
Amine Coupling Kit Cytiva Cat# BR100050
Deposited data
The density map of the RBD-VacBB-551 complex This paper EMDB: EMD-34226
The atomic model of the RBD-VacBB-551 complex This paper PDB code 8GS9
Experimental models: Cell lines
HEK-293T ATCC Cat# CRL-3216
HEK-293T-hACE2 YEASEN Biotech Cat# 41107ES03
HEK-293F Gibco Cat# R79007
Oligonucleotides
Primers used in this study (Table S4) This paper N/A
Recombinant DNA
pNL4-3.Luc.R-E− NIH AIDS Reagent Program Cat# 3418
Software and algorithms
Graphpad Prism 8.0 GraphPad https://www.graphpad.com
Biacore Evaluation software 3.0 GE Healthcare https://www.gehealthcare.com
IMGT/V-Quest IMGT http://www.imgt.org/IMGT_vquest/vquest
PyMOL PyMOL http://www.pymol.org
UCSF ChimeraX ChimeraX http://www.cgl.ucsf.edu/chimerax
Phenix Phenix http://www.phenix-online.org
Coot Coot https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot
MotionCor2 MotionCor2 https://emcore.ucsf.edu/ucsf-software
GCTF GCTF https://www2.mrc-lmb.cam.ac.uk/download/gctf_v1-06-and-examples
cryoSPARC cryoSPARC https://cryosparc.com
ColabFold v1.5.2: AlphaFold2 using MMseqs2 AlphaFold2 https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
Molprobity Molprobity http://molprobity.biochem.duke.edu
PISA v1.52 PISA https://www.ebi.ac.uk/pdbe/pisa
Origin 2023 OriginLab https://www.originlab.com
Other
Holey Carbon Grids Quantifoil Cat# R1.2/1.3 Cu400
Series S Sensor Chip CM5 Cytiva Cat# 29149603