REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
1-68 | Liu et al., 2020a | N/A |
1-87 | Liu et al., 2020a | N/A |
2-17 | Liu et al., 2020a | N/A |
2-51 | Liu et al., 2020a | N/A |
4-8 | Liu et al., 2020a | N/A |
4-18 | Liu et al., 2020a | N/A |
5-24 | Liu et al., 2020a | N/A |
4A8 | Chi et al., 2020 | N/A |
Bacterial and virus strains | ||
VSV-G pseudo-typed ΔG-luciferase | Kerafast | Cat# EH1020-PM |
Chemicals, peptides, and recombinant proteins | ||
SARS-CoV-2 spike protein | Wrapp et al., 2020b | N/A |
Polyethylenimine | Polysciences | Cat# 24765-2 |
Freestyle 293 Expression Media | Thermo Scientific | Cat# 12338-026 |
Expi293 Expression Medium | Thermo Scientific | Cat# A14635 |
Dulbecco’s Modified Eagle Medium | ATCC | Cat# 30-2002 |
Fetal Bovine Serum, heat inactivated | Thermo Scientific | Cat# 16140071 |
Opti-MEM™ Reduced Serum Media | Thermo Scientific | Cat# 31985-070 |
IMAC Sepharose 6 Fast Flow | GE Healthcare | Cat# 17092109 |
Tris Base | Thermo Scientific | Cat# BP152-5 |
Sodium Chloride | Thermo Scientific | Cat# S271-10 |
Imidazole | ACROS | Cat# 301870025 |
Series S CM5 chip | Cytiva | Cat# BR100530 |
HEPES | Sigma | Cat# H3375 |
Sodium Chloride | Thermo Scientific | Cat# S271-10 |
Tween-20 | Sigma | Cat# P7949 |
BSA | Sigma | Cat# A7906 |
His Capture kit | Cytiva | Cat# 28995056 |
Phosphoric acid | Sigma | Cat# 345245 |
Critical commercial assays | ||
FuGENE 6 | Promega | Cat# E2691 |
Strep-Tactin XT Superflow 50% | Zymo research | Cat#P2004-1-5 |
Sensor Chip CM5 | Cytiva | Cat#BR100030 |
His Capture Kit | Cytiva | Cat#28995056 |
Glycine 1.5 | Cytiva | Cat# BR100354 |
HBS-EP+ Buffer | Cytiva | Cat# BR100826 |
Spin Miniprep Kit | QIAGEN | Cat# 27106 |
Hispeed Plasmid Maxi Kit | QIAGEN | Cat# 12663 |
HisTrap Fast Flow | GE Healthcare | Cat# 17-0921-09 |
Superdex 200 Increase 10/300 GL | Cytiva | Cat# 28990945 |
HRV3C protease | Thermo Scientific | Cat# PI88946 |
Pierce™ Fab Preparation Kit | Thermo Scientific | Cat# 44985 |
EndoHf | NEB | Cat# P0703S |
Tris Base | Thermo Scientific | Cat# BP152-10 |
Calcium acetate | Sigma | Cat# 114460-21-8 |
Sodium Cacodylate | Hampton research | Cat# HR2-575 |
Glycerol | Hampton research | Cat# HR2-623 |
PEG 8000 | Sigma | Cat# 25322-68-3 |
Experimental models: Cell lines | ||
Vero E6 | ATCC | Cat# CRL-1586 |
HEK293T/17 | ATCC | Cat# CRL-11268 |
FreeStyle 293-F | Thermo Scientific | Cat# R79007 |
Expi293F Cells | Thermo Scientific | Cat# A14635 |
HEK293S GnTI- | ATCC | Cat# CRL-3022 |
I1 mouse hybridoma | ATCC | Cat# CRL-2700 |
Recombinant DNA | ||
pCMV3-SARS-CoV-2-spike | Dr. Peihui Wang, Shandong University, China | N/A |
pα-H vector | Laboratory of Daniel Leahy | N/A |
pVRC8400 vector | https://www.addgene.org | Cat#63160 |
Deposited data | ||
Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD) | This study | PDB: 7L2C |
Cryo-EM structure of NTD-directed neutralizing antibody 1-87 in complex with prefusion SARS-CoV-2 spike glycoprotein | This study | PDB: 7L2D EMDB: EMD-23125 |
Cryo-EM structure of NTD-directed neutralizing antibody 4-18 in complex with prefusion SARS-CoV-2 spike glycoprotein | This study | PDB: 7L2E EMDB: EMD-23126 |
Cryo-EM structure of NTD-directed neutralizing antibody 5-24 in complex with prefusion SARS-CoV-2 spike glycoprotein | This study | PDB: 7L2F EMDB: EMD-23127 |
Cryo-EM structure of NTD-directed neutralizing antibody 4-8 in complex with prefusion SARS-CoV-2 spike glycoprotein | This study | PDB: 7LQV EMDB: EMD-23489 |
Cryo-EM structure of NTD-directed neutralizing antibody 2-17 in complex with prefusion SARS-CoV-2 spike glycoprotein | This study | PDB: 7LQW EMDB: EMD-23490 |
Cryo-EM map of NTD-directed neutralizing antibody 1-68 in complex with prefusion SARS-CoV-2 spike glycoprotein | This study | EMDB: EMD-23150 |
Cryo-EM map of NTD-directed neutralizing antibody 2-51 in complex with prefusion SARS-CoV-2 spike glycoprotein | This study | EMDB: EMD-23151 |
Software and algorithms | ||
AIMLESS | Evans and Murshudov, 2013 | https://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html |
CCP4 | Winn et al., 2011 | https://www.ccp4.ac.uk |
Coot | Emsley and Cowtan, 2004 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot |
cryoSPARC | Punjani et al., 2017 | https://cryosparc.com |
Leginon | Suloway et al., 2005 | https://sbgrid.org/software/titles/leginon |
Molprobity | Davis et al., 2004 | http://molprobity.biochem.duke.edu |
Phaser | McCoy, 2007 | https://www.phenix-online.org/documentation/reference/phaser.html |
Phenix | Adams et al., 2010 | https://www.phenix-online.org |
The PyMOL Molecular Graphics System, Version 2.0 | Schrödinger, LLC | https://pymol.org/2/support.html#page-top |
SAbPred | Dunbar et al., 2016 | http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred |
UCSF Chimera | Pettersen et al., 2004 | https://www.cgl.ucsf.edu/chimera/ |
UCSF Chimera X | Pettersen et al., 2021 | https://www.cgl.ucsf.edu/chimerax/ |
XDS | Kabsch, 2010 | https://xds.mr.mpg.de/ |
GraphPad Prism Software | GraphPad Prism Software, Inc. | N/A |
PDBePISA | Krissinel and Henrick, 2007 | https://www.ebi.ac.uk/pdbe/pisa/ |
Scrubber 2.0 | BioLogic Software | http://www.biologic.com.au/scrubber.html |
The PyMol Molecular Graphics System, v1.8.6 | Schrödinger, LLC | https://pymol.org/2/ |
IgBLAST-1.16 | Ye et al., 2013 | https://www.ncbi.nlm.nih.gov/igblast/ |
IMGT | Schramm et al., 2016 | http://www.imgt.org/ |
MUSCLE v3.8.31 | Edgar, 2004 | https://www.drive5.com/muscle/manual/install.html |
SONAR v2.0 | Schramm et al., 2016 | https://github.com/scharch/sonar/ |
Python v3.8.3 | https://www.python.org/ | |
The R Project for Statistical Computing | https://www.r-project.org/ | |
R bio3d package | Grant et al., 2006 | http://thegrantlab.org/bio3d/ |
MAFFT | Katoh et al., 2002 | https://mafft.cbrc.jp/alignment/software/ |
FreeSASA v2.0.3 | Mitternacht, 2016 | https://freesasa.github.io/ |