REAGENT or RESOURCE	SOURCE	IDENTIFIER
Anitibodies
Allophycocyanin (APC) AffiniPure F(ab’)2 Fragment Goat Anti-Human IgG, Fcγ fragment specific	Jackson	RRID: AB_2337695
AffiniPure Goat Anti-Mouse IgG, Fcγ fragment specific	Jackson	RRID: AB_2338449
Anti-ACE-2, Mouse-Mono(535919)	R&D	Cat#MAB9332-100
Allophycocyanin (APC) Streptavidin	Jackson	RRID: AB_2337242
APC anti-FLAG Tag Antibody (L5)	Biolegend	Cat#637308
Allophycocyanin (APC) AffiniPure F(ab’)2 Fragment Donkey Anti-Rat IgG (H+L)	Jackson	RRID: AB_2340661
R-Phycoerythrin AffiniPure F(ab’)2 Fragment Goat Anti-Human IgG, F(ab’)2 fragment specific	Jackson	RRID: AB_2337677
Chemicals, peptides, and recombinant proteins
Propidium iodide	Sigma-Aldrich	Cat#25535-16-4
PEI-MAX	Polyscience	Cat#26406
TALON metal affinity resin	Clontech	Cat#635503
Aldehyde/Sulfate Latex Beads, 4% w/v, 4 μm	Thermo Fisher	Cat#A37304
DOTAP	Sigma-Aldrich	Cat#144189-73-1
protein A Sepharose	GE Healthcare	Cat#17127903
Sulfo-NHS-LC-Biotin	Thermo Fisher	Cat#21335
DyLight 650 NHS Ester	Thermo Fisher	Cat#62265
4% paraformaldehyde	Nacalai Tesque	Cat#09154-85
Wizard Plus SV Minipreps DNA Purification System	promega	Cat#A1465
QIAGEN Plasmid Plus Midi Kit	QIAGEN	Cat#12945
QIAamp viral RNA extraction kit	QIAGEN	Cat# 52904
QuikChange Lightning Multi Site-Directed Mutagenesis Kit	Agilent	Cat#210513-5
Immobilized Pepsin	Thermo Fisher	Prod# 20343
Papain Agarose from papaya latex	Sigma-Aldrich	Prod# P4406
Vivaspin 6, 50,000 MWCO PES	Sartorius	Cat#VS0632
Oriole Fluorescent Gel Stain	Bio-Rad	Cat#1610496
e-PAGEL E-R520L	Atto	Cat#2331730
Zeba Spin Desalting Columns, 7K MWCO, 0.5 mL	Thermo Fisher	Cat#89882
Deposited data
Cryo-EM map of Apo spike protein	This paper	EMD-30915
Cryo-EM map of spike protein with 8D2 Fab fragment	This paper	EMD-30916
Cryo-EM map of spike protein with (8D2)-1 Fab fragment	This paper	EMD-30917
Cryo-EM map of spike protein with (8D2)-2 Fab fragment	This paper	EMD-30918
Cryo-EM map of spike protein with (8D2)-3 Fab fragment	This paper	EMD-30919
Cryo-EM map of spike protein with (8D2)-4 Fab fragment	This paper	EMD-30920
Cryo-EM map of spike protein with (COV2-2490)-1 Fab fragment	This paper	EMD-30921
Cryo-EM map of spike protein with (COV2-2490)-2 Fab fragment	This paper	EMD-30922
Molecular model fitted to Cryo-EM data of Apo spike protein	This paper	7DZW
Molecular model fitted to Cryo-EM data of spike protein with 8D2 Fab fragment	This paper	7DZX
Molecular model fitted to Cryo-EM data of spike protein with COV2-2490 Fab fragment	This paper	7DZY
Experimental models: Cell lines
293T	RIKEN Cell Bank	RCB2202
VERO	Japanese Collection of Research Bioresources	JCRB1819
Huh7	National Institute of Infectious Diseases	N/A
293T-ACE2	This paper	N/A
PLAT-E	https://doi.org/10.1038/sj.gt.3301206	N/A
Expi293	Thermo	A14527
Bacterial and virus strains
SARS-CoV-2 WA-1	Kanagawa Prefectural Institute of Public Health	KNG19-020
Biological samples
SARS-CoV-2 patients serum	Kobe City Medical Center General Hospital	N/A
Normal humans serum (Taken before June 2019)	George King Bio-Medical	0070-50 (Lot 1125)
Recombinant DNA
pcDNA3.4 Spike-foldon-his	This paper	N/A
pME18S ACE2-Fc	This paper	N/A
pME18S Spike	This paper	N/A
pME18S Spike D614G	This paper	N/A
pME18S Flag-NTD-TM	This paper	N/A
pME18S Flag-RBD-TM	This paper	N/A
pME18S Flag-S2-TM	This paper	N/A
pME18S Flag B.1.1.7 variants Spike (del_70-69, del_144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H)	This paper	N/A
pMxs-ACE2	This paper	N/A
pME18S-FLAG-COVID-S	This paper	N/A
pME18S Flag-NTD-TM	This paper	N/A
pME18S-FLAG-COVID-S-V213A	This paper	N/A
pME18S-FLAG-COVID-S-H66A	This paper	N/A
pME18S-FLAG-COVID-S-W64A	This paper	N/A
pME18S-FLAG-COVID-S-K187A	This paper	N/A
pME18S-FLAG-COVID-S-R214A	This paper	N/A
pME18S-FLAG-COVID-S-W64A H66A	This paper	N/A
pME18S-FLAG-COVID-S-V213A R214A	This paper	N/A
pME18S-FLAG-COVID-S-W64A H66A V213A R214A	This paper	N/A
pME18S-FLAG-NTD-TM-K187A	This paper	N/A
pME18S-FLAG-NTD-TM-Y28A	This paper	N/A
pME18S-FLAG-NTD-TM-T29A	This paper	N/A
pME18S-FLAG-NTD-TM-N30A	This paper	N/A
pME18S-FLAG-NTD-TM-S31A	This paper	N/A
pME18S-FLAG-NTD-TM-F32A	This paper	N/A
pME18S-FLAG-NTD-TM-T63A	This paper	N/A
pME18S-FLAG-NTD-TM-W64A	This paper	N/A
pME18S-FLAG-NTD-TM-F65A	This paper	N/A
pME18S-FLAG-NTD-TM-H66A	This paper	N/A
pME18S-FLAG-NTD-TM-I68A	This paper	N/A
pME18S-FLAG-NTD-TM-H69A	This paper	N/A
pME18S-FLAG-NTD-TM-K77A	This paper	N/A
pME18S-FLAG-NTD-TM-R78A	This paper	N/A
pME18S-FLAG-NTD-TM-S94A	This paper	N/A
pME18S-FLAG-NTD-TM-T95A	This paper	N/A
pME18S-FLAG-NTD-TM-E96A	This paper	N/A
pME18S-FLAG-NTD-TM-K97A	This paper	N/A
pME18S-FLAG-NTD-TM-I100A	This paper	N/A
pME18S-FLAG-NTD-TM-K113A	This paper	N/A
pME18S-FLAG-NTD-TM-K147A	This paper	N/A
pME18S-FLAG-NTD-TM-K150A	This paper	N/A
pME18S-FLAG-NTD-TM-R158A	This paper	N/A
pME18S-FLAG-NTD-TM-K182A	This paper	N/A
pME18S-FLAG-NTD-TM-N185A	This paper	N/A
pME18S-FLAG-NTD-TM-F186A	This paper	N/A
pME18S-FLAG-NTD-TM-K187A	This paper	N/A
pME18S-FLAG-NTD-TM-N211A	This paper	N/A
pME18S-FLAG-NTD-TM-L212A	This paper	N/A
pME18S-FLAG-NTD-TM-V213A	This paper	N/A
pME18S-FLAG-NTD-TM-R214A	This paper	N/A
pME18S-FLAG-NTD-TM-D215A	This paper	N/A
pME18S-FLAG-NTD-TM-R237A	This paper	N/A
pME18S-FLAG-NTD-TM-R246A	This paper	N/A
pME18S-FLAG-NTD-TM-D253A	This paper	N/A
pME18S-FLAG-NTD-TM-S255A	This paper	N/A
pCAGGS H014-human IgG1	This paper (related to Lv et al., 2020)	N/A
pCAGGS H014-human Kappa	This paper (related to Lv et al., 2020)	N/A
pCAGGS COV2-2016-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2026-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2146-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2150-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2190-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2212-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2210-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2202-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2215-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2222-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2228-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2248-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2293-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2335-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2369-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2384-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2420-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2438-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2459-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2490-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2495-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2521-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2563-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2571-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2582-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2622-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2660-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2673-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2718-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2830-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS 4A8-human IgG1	This paper (related to Chi et al., 2020)	N/A
pCAGGS 8D2-human IgG1	This paper (related to Chi et al., 2020)	N/A
pCAGGS 4A2-human IgG1	This paper (related to Chi et al., 2020)	N/A
pCAGGS COV2-2697-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2241-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS 2-02-human IgG1	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS C002-human IgG1	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS 2-04-human IgG1	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 2-07-human IgG1	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS C009-human IgG1	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS 1-12-human IgG1	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 2-15-human IgG1	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 1-16-human IgG1	This paper (Brouwer et al., 2020)	N/A
pCAGGS 1-18-human IgG1	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 2-29-human IgG1	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS C101-human IgG1	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS C121-human IgG1	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS C135-human IgG1	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS C144-human IgG1	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS COV2-2675-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2027-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2496-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2400-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2445-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2147-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2570-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2373-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2035-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2383-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2784-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2454-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2947-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2656-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2553-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2238-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2143-human IgG1	This paper (related to Zost et al., 2020)	N/A
pCAGGS 4A10-human IgG1	This paper (related to Chi et al., 2020)	N/A
pCAGGS 7E9-human IgG1	This paper (related to Chi et al., 2020)	N/A
pCAGGS COV2-2016-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2026-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2146-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2150-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2190-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2212-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2210-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2202-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2215-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2222-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2228-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2248-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2293-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2335-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2369-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2384-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2420-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2438-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2459-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2490-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2495-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2521-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2563-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2571-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2582-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2622-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2660-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2673-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2718-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2830-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS 4A8-human Kappa	This paper (related to Chi et al., 2020)	N/A
pCAGGS 8D2-human Kappa	This paper (related to Chi et al., 2020)	N/A
pCAGGS 4A2-human Kappa	This paper (related to Chi et al., 2020)	N/A
pCAGGS COV2-2697-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2241-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS 2-02-human Kappa	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS C002-human Kappa	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS 2-04-human Kappa	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 2-07-human Kappa	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS C009-human Kappa	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS 1-12-human Kappa	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 2-15-human Kappa	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 1-16-human Kappa	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 1-18-human Kappa	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS 2-29-human Kappa	This paper (related to Brouwer et al., 2020)	N/A
pCAGGS C101-human Kappa	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS C121-human Kappa	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS C135-human Kappa	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS C144-human Kappa	This paper (related to Robbiani et al., 2020)	N/A
pCAGGS COV2-2675-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2027-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2496-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2400-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2445-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2147-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2570-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2373-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2035-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2383-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2784-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2454-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2947-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2656-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2553-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2238-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2143-human Kappa	This paper (related to Zost et al., 2020)	N/A
pCAGGS 4A10-human Kappa	This paper (related to Chi et al., 2020)	N/A
pCAGGS 7E9-human Kappa	This paper (related to Chi et al., 2020)	N/A
pCAGGS COV2-2210-mouse IgG2a	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2369-mouse IgG2a	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2490-mouse IgG2a	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2582-mouse IgG2a	This paper (related to Zost et al., 2020)	N/A
pCAGGS COV2-2660-mouse IgG2a	This paper (related to Zost et al., 2020)	N/A
pCAGGS 8D2-mouse IgG2a	This paper (related to Chi et al., 2020)	N/A
Software and algorithms
FlowJo10	Becton Dicknson	N/A
Prism7.0	GraphPad	N/A
cryoSPARC	Structura Biotechnology	N/A