| Strain, strain background (HIV-1) |
HIV Env clone BG505.W6M.C2 T332N |
Wu et al., 2006
|
GenBank: DQ208458.1
|
|
| Strain, strain background (HIV-1) |
HIV Env clone SF162 |
Cheng-Mayer et al., 1997
|
GenBank: EU123924.1
|
|
| Strain, strain background (HIV-1) |
HIV Env clone QC406.70M.F3 |
Blish et al., 2009
|
Genbank: FJ866133.1
|
|
| Strain, strain background (HIV-1) |
HIV Env clone QA013.765M.C1 |
Williams et al., 2018
|
Genbank: MG992331
|
|
| Strain, strain background (HIV-1) |
QB726.70M.B3 |
Blish et al., 2009
|
Genbank: FJ866111.1
|
|
| Strain, strain background (HIV-1) |
Q259.W6 |
Long et al., 2002
|
Genbank: AF407151.1
|
|
| Strain, strain background (HIV-1) |
QH343.21M.A10 |
Blish et al., 2009
|
Genbank: FJ866119.1
|
|
| Strain, strain background (HIV-1) |
QA255.21P.A15 |
Bosch et al., 2010
|
Genbank: MW383929.1
|
|
| Strain, strain background (HIV-1) |
BI206.W6RT.A1 |
Wu et al., 2006
|
Genbank: DQ208465.1
|
|
| Strain, strain background (HIV-1) |
BF520.W14.B3 |
Simonich et al., 2016
|
Genbank: KX168093.1
|
|
| Strain, strain background (HIV-1) |
BL274.W6.A3 |
Wu et al., 2006
|
Genbank: DQ208499.1
|
|
| Strain, strain background (HIV-1) |
ML274.W0.D1 |
Wu et al., 2006
|
Genbank: DQ208495.1
|
|
| Strain, strain background (HIV-1) |
MS208.W0.B.A3 |
Wu et al., 2006
|
Genbank: DQ187022.1
|
|
| Strain, strain background (HIV-1) |
MI206.W0.A1 |
Wu et al., 2006
|
Genbank: DQ208459.1
|
|
| Strain, strain background (HIV-1) |
MJ613.W1.A2 |
Wu et al., 2006
|
Genbank: DQ208444.1
|
|
| Strain, strain background (HIV-1) |
MG505.W0.A2 |
Wu et al., 2006
|
Genbank: DQ208449.1
|
|
| Strain, strain background (HIV-1) |
MF535.W0.F1 |
Wu et al., 2006
|
Genbank: DQ208429.1
|
|
| Strain, strain background (HIV-1) |
ML035.W0.A1 |
Wu et al., 2006
|
Genbank: DQ208468.1
|
|
| Strain, strain background (HIV-1) |
BF535.W6.A1 |
Wu et al., 2006
|
Genbank: DQ208431.1
|
|
| Strain, strain background (HIV-1) |
BL035.W6.B1 |
Wu et al., 2006
|
Genbank: DQ208479.1
|
|
| Strain, strain background (HIV-1) |
MK184.W0.D1 |
Wu et al., 2006
|
Genbank: DQ208484.1
|
|
| Strain, strain background (HIV-1) |
QA465.59M.A1 |
Blish et al., 2009
|
Genbank: FJ866136.1
|
|
| Strain, strain background (HIV-1) |
QB857.110I.B3 |
Blish et al., 2009
|
Genbank: FJ866138.1
|
|
| Strain, strain background (Escherichia coli) |
One Shot Top10 |
Thermo Fisher |
Cat#C404003 |
chemically competent cells |
| Cell line (Homo sapiens) |
FreeStyle 293F |
Invitrogen |
Cat#R790-07; RRID:CVCL_D603
|
|
| Cell line (Homo sapiens) |
Human Embryonic Kidney (HEK) 293T |
ATCC |
Cat# CRL-3216; RRID:CVCL_0063
|
|
| Cell line (Homo sapiens) |
TZM-bl |
AIDS Reagent Program, Division of AIDS, NIAID, NIH. |
Cat# ARP-8129; RRID:CVCL_B478
|
|
| Biological sample (Homo sapiens) |
Human PBMC samples from subject QA013 |
Martin et al., 1998
|
N/A |
|
| Antibody |
VRC01 (human, monoclonal) |
Williams et al., 2019
|
N/A |
ELISA, tested at 25 µg/mL |
| Antibody |
NIH 45–46 (human, monoclonal) |
Scheid et al., 2009
|
N/A |
ELISA, tested at 25 µg/mL |
| Antibody |
8ANC195 (human, monoclonal) |
Scheid et al., 2011
|
N/A |
ELISA, tested at 25 µg/mL |
| Antibody |
4E10 (human, monoclonal) |
Stiegler et al., 2001
|
N/A |
ELISA, tested at 25 µg/mL |
| Antibody |
Fi6v3 (human, monoclonal) |
Jesse Bloom |
N/A |
ELISA, tested at 25 µg/mL |
| Recombinant DNA reagent |
Human Igγ1 expression vector |
Tiller et al., 2008
|
Addgene: 80795 |
|
| Recombinant DNA reagent |
Human Igκ expression vector |
Tiller et al., 2008
|
Addgene: 80796 |
|
| Recombinant DNA reagent |
Human Igλ expression vector |
Tiller et al., 2008
|
Addgene: 99575 |
|
| Peptide, recombinant protein |
BG505.SOSIP.664 |
Sanders et al., 2013; Verkerke et al., 2016
|
Courtesy of Kelly Lee |
|
| Peptide, recombinant protein |
Protein G agarose |
Pierce |
Cat#20397 |
|
| Peptide, recombinant protein |
BG505.W6.C1 gp120 monomer |
Immune Technology Corp. |
Cat#IT-001–176 p |
|
| Peptide, recombinant protein |
QA013.70I.H1 gp120 monomer |
Cambridge Biologics |
GenBank: MG992347
|
custom protein synthesis |
| Peptide, recombinant protein |
QA013.765M.C1 gp120 monomer |
Cambridge Biologics |
Genbank: MG992331
|
custom protein synthesis |
| Commercial assay or kit |
Gal-Screen |
Thermo Fisher |
Cat#T1028 |
|
| Commercial assay or kit |
AllPrep DNA/RNA Mini Kit |
Qiagen |
Cat#80204 |
|
| Commercial assay or kit |
SMARTer RACE 5’/3’ Kit |
Takara Bio USA |
Cat#634858 |
|
| Commercial assay or kit |
KAPA library quantification kit |
Kapa Biosystems |
Cat#KK4824 |
|
| Commercial assay or kit |
600-cycle MiSeq Reagent Kit v3 |
Illumina |
Cat#MS-102–3003 |
|
| Commercial assay or kit |
Nextera XT 96-well index kit |
Illumina |
Cat#FC-131–1001 |
|
| Commercial assay or kit |
QIAquick PCR Purification Kit |
Qiagen |
Cat#28104 |
|
| Chemical compound, drug |
FreeStyle MAX |
Thermo Fisher |
Cat#16447500 |
|
| Chemical compound, drug |
293F FreeStyle Expression media |
Invitrogen |
Cat#12338–026 |
|
| Chemical compound, drug |
Q5 High-Fidelity Master Mix |
New England BioLabs |
Cat#M0492S |
|
| Chemical compound, drug |
DEAE-dextran |
VWR |
Cat#97061–684 |
|
| Software, algorithm |
FLASH v1.2.11 |
Magoč and Salzberg, 2011
|
http://ccb.jhu.edu/software/FLASH/
|
|
| Software, algorithm |
Cutadapt 1.14 with Python 2.7.9 |
Martin, 2011
|
http://cutadapt.readthedocs.io/en/stable/
|
|
| Software, algorithm |
FASTX toolkit 0.0.14 |
Hannon Lab, Cold Spring Harbor |
http://hannonlab.cshl.edu/fastx_toolkit/
|
|
| Software, algorithm |
Partis |
Ralph and Matsen, 2016
|
https://github.com/psathyrella/partis
|
|
| Software, algorithm |
FastTree 2 |
Price et al., 2010
|
https://github.com/matsengrp/cft/blob/master/bin/prune.py
|
|
| Software, algorithm |
Linearham |
Dhar et al., 2020
|
https://github.com/matsengrp/linearham
|
|
| Software, algorithm |
RevBayes |
Höhna et al., 2016, Höhna et al., 2021
|
https://revbayes.github.io/
|
|
| Software, algorithm |
Local BLAST |
Biopython |
https://github.com/matsengrp/cft/blob/master/bin/blast.py
|
|
| Software, algorithm |
WebLogo |
Crooks et al., 2004
|
RRID:SCR_010236
|
|
| Software, algorithm |
Geneious v11.1.2 |
Kearse et al., 2012
|
RRID:SCR_010519
|
|
| Software, algorithm |
Excel |
Microsoft |
RRID:SCR_016137
|
|
| Software, algorithm |
ForteBio’s Octet Software ‘Data Analysis 7.0’ |
Pall ForteBio (now Sartorius) |
N/A |
|
| Software, algorithm |
Prism 9.0 |
GraphPad |
RRID:SCR_002798
|
|
| Software, algorithm |
Relion v3.0.7 |
Scheres, 2012
|
RRID:SCR_016274
|
|
| Software, algorithm |
MotionCor2 |
Zheng et al., 2017
|
RRID:SCR_016499
|
|
| Software, algorithm |
CTFFIND4 |
Rohou and Grigorieff, 2015
|
RRID:SCR_016732
|
|
| Software, algorithm |
UCSF Chimera |
Pettersen et al., 2004
|
RRID:SCR_004097
|
|
| Software, algorithm |
SWISS-MODEL |
Waterhouse et al., 2018
|
RRID:SCR_013032
|
|
| Software, algorithm |
Phenix software suite |
Liebschner et al., 2019
|
RRID:SCR_014224
|
Autosharpen program (Terwilliger et al., 2018); ‘Dock In Map’ program; Realspace RefinementOo |
| Other |
Anti-human IgG Fc capture biosensors |
Sartorius |
Cat#18–5063 |
|
| Other |
QA013 antibody variable gene sequencing data |
This paper |
BioProject SRA: PRJNA674442 |
|
| Other |
cryo-EM map and atomic coordinates |
This paper |
EMD-24195 and PDB 7N65 |
|
