REAGENT or RESOURCES	SOURCE	IDENTIFIER
Bacterial and virus strains
DH5α Chemically Competent Cell	Invitrogen	Cat#12034013
G∗ΔG-VSV	Kerafast	Cat#EH1020-PM
Cell lines
HEK293F cells	Thermo Fisher	Cat # 11625019
Huh7 cells	NIFDC	N/A
Chemicals, peptides, and recombinantproteins
RPMI 1640 Medium	Thermo Fisher	Cat # 12633012
Trypsin	Thermo Fisher	Lot# TG269188
DMEM	Thermo Fisher	Cat#11965092
1x PBS, pH 7.4	Thermo Fisher	Cat # 10010031
Fetal bovine serum (FBS)	Thermo Fisher	Cat # 10099
D-luciferin	Thermo Fisher	Cat # L2916
Uranyl Formate	Electron Microscopy China	Cat # GZ02625
Critical commercial reagents
Superose 6 Increase 10/300 GL	GE healthcare	Cat # 29091596
SYPRO protein gel stain	Thermo Fisher	Cat # S6650
NiNTA Biosensors	Octet	Cat # 18-5102
AR2G Biosensors	Octet	Cat # 18-5095
CM5 Biosensor	Cytiva	Lot # 10310113
Recombinant DNA
SARS-CoV-2 S gene, residues 1-1208, pcDNA	GenScript ProBio	GenBank: MN908947
SARS-CoV-2 Delta S gene, residues 1-1208, 6P and T19R, G142D, EF156-157del, R158G, L452R, T478K, D614G, P681R, D950N, T4 fibritin trimerization motif,6xHis, pcDNA	This manuscript	N/A
SARS-CoV-2 Omicron S gene, residues 1-1208, 6P and A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F, T4 fibritin trimerization motif,6xHis, pcDNA	This manuscript	N/A
Deposited data
Local map of Omicron S-trimer in complex with ACE2	This manuscript	PDB ID 7WGC, EMD-32483
Omicron S-trimer in complex with ACE2	This manuscript	PDB ID 7WGB, EMD-32482
Delta S-trimer (1 RBD Up)	This manuscript	PDB ID 7WG9, EMD-32481
Delta S-trimer (3 RBD Down)	This manuscript	PDB ID 7WG8, EMD-32480
Omicron S-trimer at pH 5.5	This manuscript	PDB ID 7WG7, EMD-32479
Omicron S-trimer at pH 7.5	This manuscript	PDB ID 7WG6, EMD-32478
Software
igraph (1.2.5)	N/A	https://cran.r-project.org/web/packages/igraph/index.html
Gctf program (v1.06)	N/A	https://www2.mrc-lmb.cam.ac.uk/download/gctf/
RELION (v3.07)	Zivanov et al., 2018	https://www2.mrc-lmb.cam.ac.uk/relion
UCSF Chimera	N/A	https://www.cgl.ucsf.edu/chimera
UCSF ChimeraX	N/A	https://www.rbvi.ucsf.edu/chimerax/
PHENIX	N/A	https://www.phenix-online.org
Coot	N/A	https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot
cryoSPARC 3.2.4	N/A	https://cryosparc.com