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. Author manuscript; available in PMC: 2022 Apr 5.
Published in final edited form as: Cell Rep. 2022 Mar 1;38(9):110436. doi: 10.1016/j.celrep.2022.110436

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
PGT145 NIH AIDS Reagent Program Cat# ARP-12703; RRID: AB_2491054
PGT151 Laboratory of Dr. Genevieve Giny Fouda, Duke University (Falkowska et al., 2014) N/A
PG9 NIH AIDS Reagent Program Cat# ARP-12149; RRID: AB_2491030
PG16 NIH AIDS Reagent Program Cat# ARP-12150; RRID: AB_2491031
PGT121 NIH AIDS Reagent Program Cat# ARP-12343; RRID: AB_2491041
447-52D NIH AIDS Reagent Program Cat# ARP-4030; RRID: AB_2491016
48d NIH AIDS Reagent Program Cat# ARP-1756; RRID: AB_2905601
39f NIH AIDS Reagent Program Cat# ARP-11437; RRID: AB_2905602
17b NIH AIDS Reagent Program Cat# ARP-4091; RRID: AB_2905603
CAP256-VRC26.08 Laboratory of Dr. Genevieve Giny Fouda, Duke University (Doria-Rose et al., 2014) N/A
NIH45-46G54W NIH AIDS Reagent Program Cat# ARP-12174; RRID: AB_2491035
3BNC117 Cat# ARP-12474; RRID: AB_2491033
CD4-IgG2 NIH AIDS Reagent Program Cat# 11780; RRID: AB_2905604
PGDM1400 Laboratory of Dr. Genevieve Giny Fouda, Duke University (Sok et al., 2014) N/A
CAP228-16H Laboratory of Dr. Lynn Morris, Wits University (van Eeden et al., 2018) N/A
697-30D NIH AIDS Reagent Program Cat# ARP-7371; RRID: AB_2905605
ID6 NIH AIDS Reagent Program Cat# ARP-2343; RRID: AB_2905606
Mouse Anti-human biotin BD Biosciences Cat# 555785; RRID: AB_396120
Goat anti-mouse-HRP Southern Biotech Cat#1030-05; RRID: AB_2619742
Goat anti-rabbit HRP Southern Biotech Cat# 4010-05; RRID: AB_2632593
Streptavidin HRP Vector Labs Cat#SA5004; RRID: AB_2336509
Goat anti-rabbit IgG PE Southern Biotech Cat#4030-09; RRID: AB_2795937
Anti-p27 2F12 NIH AIDS Reagent Program Cat# ARP-1610; RRID: AB_2905607
Goat anti-mouse IgG2b Southern Biotech Cat# 1090-05; RRID: AB_2794521
Biotinylated Anti-SIV IgG Laboratory of Dr Pam Kozlowski, LSUHSC School of Medicine (Jensen et al., 2016) N/A
EM4C04 Anti-Influenza Ab Laboratory of Dr. Jens Wrammert, Emory University (O’Donnell et al., 2012) N/A
Bacterial and viral strains
Bacteria: NEB® 5-alpha Competent E. coli (High Efficiency) NEB Cat# C2987H
Bacteria: NEB® Stable Competent E. coli cells NEB Cat# C3040H
Tier2 Clade C SHIV1157ipd3N4 virus Laboratory of Dr. Ruth Ruprecht and the HIV reagent resource Cat# ARP-11689
Biological Samples
Serum samples from Rabbits This Manuscript N/A
Human PBMCs This Manuscript N/A
Chemicals, peptides, and recombinant proteins
C.1086 NFL (with I559P) Guenaga et al., 2017 N/A
C.1086 SOSIP This Manuscript N/A
C.1086 UFO (no disulphide linkage between A501 and T605) He et al., 2018 N/A
C.1086 UFO-v2 This Manuscript N/A
C.1086 UFO-v2-RHH173 This Manuscript N/A
C.1086 UFO-v2-RQH173 This Manuscript N/A
C.1086 UFO-v2-RQY173 This Manuscript N/A
C.1086 UFO-v2-V2-HS mutants This Manuscript N/A
C.1086 UFO-v2-RQH173 Avi This Manuscript N/A
C.1086 UFO-v2-RQY173 Avi This Manuscript N/A
BG505 SOSIP.664 WT Sanders et al., 2013 N/A
BG505 SOSIP.664 KQY This Manuscript N/A
BG505 SOSIP.664 RHY This Manuscript N/A
BG505 SOSIP.664 KHY This Manuscript N/A
gp70 C.1086 RQH173 V1V2 This Manuscript N/A
gp70 C.1086 RQY173 V1V2 This Manuscript N/A
gp70 V1V2 global panel Zolla-Pazner et al., 2014 N/A
C.1086 V3 peptide NTRPNNNT RKSIRIGPGQTFYA TGDIIGNIRQAHC This Manuscript N/A
Phusion High-Fidelity PCR Master Mix with HF Buffer ThermoScientific Cat# F531S
T4 DNA Ligase NEB Cat# M0202S
T4 Polynucleotide Kinase NEB Cat# M0201S
DpnI NEB Cat# R0176S
NheI-HF NEB Cat# R3131S
ClaI NEB Cat# R0197S
Galanthus nivalis lectin-agarose Vector Laboratories Cat# AL-1243-5
Expifectamine™ 293 transfection kit ThermoScientific Cat# A14524
Expi293™ Expression Medium ThermoScientific Cat# A1435101
cOmplete™, Mini Protease Inhibitor Cocktail Millipore Sigma Cat# 11836153001
Methyl α-D-mannopyranoside Millipore Sigma Cat# M6882-25G
Superdex 200 Increase 10/300 GL Cytiva (GE Healthcare LifeSciences) Cat# GE28-9909-44
Amicon Ultra-4, MWCO 100kDa Millipore Sigma Cat# UFC910024
Pierce™ Protein A IgG Purification Kit, 1 mL ThermoScientific Cat# 44667
NuPAGE™, 4-12% Bis-Tris Protein Gels ThermoScientific Cat# NP0321BOX
NativeMark™ Unstained Protein Standard ThermoScientific Cat# LC0725
DMEM (Dulbecco’s Modified Eagle’s Medium) Corning Cat# 10-013-CV
HyClone™ Fetal Bovine Serum (FBS) Cytiva (GE Healthcare LifeSciences) Cat# SH30910.03
10X Kinetics Buffer Pall ForteBio Cat# 18-5032
Slide-A-Lyzer™ Dialysis Cassettes, 20K MWCO, 30 mL ThermoScientific Cat# 66030
Lipofectamine™ 2000 Transfection Reagent Thermo Scientific Cat# 11668019
Amicon® Ultra-15 Centrifugal Filter Unit, 30KDa, 24 Millipore Cat# UFC903024
Precision Plus Protein™ Kaleidoscope™ Prestained Protein Standards BioRad Cat# 1610375
Microplate, 384 well, PP, Black, F-Bottom Greiner Cat# 781209
ELISA maxisorp microtiter plates ThermoFisher Cat# 439454
Concanavalin A (ConA) Millipore Sigma Cat# C2272
Blotting-grade Blocker (contains BSA) Biorad Cat# 1706404
Whey from bovine milk, spray dried Millipore Sigma Cat# W1500-2.5KG
Opti-MEM™ Reduced Serum medium ThermoScientific Cat# 31985070
Streptavidin horseradish peroxidase Vector Laboratories Cat# SA5004; RRID: AB_2336509
NativePAGE™ 20X Running Buffer ThermoScientific Cat# BN2001
Imidazole Millipore Sigma Cat# I5513-25G
Tween-20 Millipore Sigma Cat# P7949
EconoPac disposable chromatography columns Biorad Cat# 7321010
PP Microplate 384 well, F-Shape, Black 128/85/15mm Greiner Cat# 781209
PBS (1X) Corning Cat# 21040-CV
HEPES Millipore Sigma Cat# H4034
Ampicillin sodium salt Millipore Sigma Cat# A9518
Kanamycn sulphate Millipore Sigma Cat# 60615
96-well Clear V-Bottom TC-treated Microplate Corning Cat# 3894
LIVE/DEAD™ Fixable Far Red Dead Cell Stain Kit, for 633 or 635 nm excitation ThermoScientific Cat# L34973
D2O Millipore Sigma Cat# 151882
Formic Acid Millipore Sigma Cat# 27001
TritonX-100 Millipore Sigma Cat# T9284
Uranyl formate Electron Microscopy Sciences Cat# 22451
neutralite-avidin peroxidase (N-HRP) Southern Biotech Cat# 7200-05
Critical commercial assays
Pierce™ BCA Protein Assay Kit ThermoScientific Cat# 23227
KPL TMB Microwell Peroxidase Substrate System SeraCare Cat# 5120-0047
HIV-1 p24 ELISA Kit Abcam Cat# ab218268
britelite plus Reporter Gene Assay System PerkinElmer Cat# 6066761
Deposited data
Native gel image of C.1086 variants This Manuscript https://doi.org/10.17632/9zp2hh598z.1
Experimental models: Cell lines
FreeStyle 293F Invitrogen Cat# R79007; RRID: CVCL_D603
TZM-bl NIH AIDS Reagent Program Cat# 8129; RRID: CVCL_B478
HEK 293T ATCC Cat# CRL-3216; RRID: CVCL_0063
CEM-NKr CCR5+ NIH AIDS Reagent Program Cat# 4376; RRID: CVCL_X622
Experimental models: Organisms/strains
Rabbit: New Zealand White female Covance N/A
Oligonucleotides
N279Q_For 5′-CAAAATGCCAAAACAATAATAGTACAC-3′ This Manuscript N/A
N279Q_Rev 5′-TGTCAGATTTTCAGATCTAATTATTATCTCTTC-3′ This Manuscript N/A
N280D_For 5′-GATGCCAAAACAATAATAGTACACC-3′ This Manuscript N/A
N280D_Rev 5′-GTTTGTCAGATTTTCAGATCTAATTATTATCTC-3′ This Manuscript N/A
G459E_For 5′-GAGCAATCAAATGAAACAAATGACAC-3′ This Manuscript N/A
G459_rev 5′-TCCATCACGTAGCAATAGTAGTC-3′ This Manuscript N/A
G458Y_For 5′-TATGGTCAATCAAATGAAACAAATGAC-3′ This Manuscript N/A
G458Y_Rev 5′-ATCACGTAGCAATAGTAGTCCTG-3′ This Manuscript N/A
S365K_For 5′-AAAGGAGGGGATCTAGAAATTAC-3′ This Manuscript N/A
S365K_Rev 5′-GGATGGTTCAAACTTTATTGTTTTACTAG-3′ This Manuscript N/A
T162A_For 5′-GCGACGGAACTAAGAGATAAAAAAC-3′ This Manuscript N/A
T162A_Rev 5′-TGCATTGAAAGAGCAATTTTTCATTACTTC-3′ This Manuscript N/A
D167A_For 5′-GCGAAAAAACAAAAGGTGCAT-3′ This Manuscript N/A
D167A_Rev 5′-TCTTAGTTCCGTGGTTGC-3′ This Manuscript N/A
For_N156A 5′-GCATGCTCTTTCAATGCAACC-3′ This Manuscript
Rev_156 5′-TTTCATTACTTCACTGGTGTCACTC-3′ This Manuscript N/A
For_173A 5′-GCAGCGCTTTTTTATAAACTTGATGTAG-3′ This Manuscript N/A
Rev_173 5′-CAATGCAACCACGGAACTAAG-3′ This Manuscript N/A
For_181A 5′-GCAGTACCACTTAATGGAAACAG-3′ This Manuscript N/A
Rev_181A 5′-ATCAAGTTTATAAAAAAGCGCATGCAC-3′ This Manuscript N/A
Recombinant DNA
pSV-A-MLV-env NIH AIDS Reagent program Cat# ARP-1065
pCDNA3.1_C.1086 K160N RQH S365K This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH D167A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH G458Y This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH N279Q This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH T162A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH N280D This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH G459E This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH G459P This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH This Manuscript N/A
pCDNA3.1_C.1086 K160N RQY This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH I371A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH R166A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH N156A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH 611A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH 160A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH 160K This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH 332A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH 181A This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH 166K This Manuscript N/A
pCDNA3.1_C.1086 K160N RQH 173A This Manuscript N/A
pGA1_C.1086_WT_gp140 This Manuscript N/A
pGA1_C.1086_NFL_gp140 This Manuscript N/A
pGA1_C.1086_UFO_gp140 This Manuscript N/A
pGA1_C.1086_UFO_v2_RHH_gp140 This Manuscript N/A
pGA1_C.1086_UFO_v2_RHH_gp140 This Manuscript N/A
pGA1_C.1086_UFO_v2-RQY_gp140 This Manuscript N/A
pGA1_BG505_SOSIP_V2-HS mutants This Manuscript N/A
pGA1_C.1086_UFO_v2_V2-HS mutants This Manuscript N/A
pGA1_BG505_SOSIP_gp140 This Manuscript N/A
pCDNA3.1_C.1086 K160N Laboratory of Dr. Cynthia Derdeyn, Emory University (Burton et al., 2019) N/A
Software and algorithms
ForteBio Octet Data Analysis v9 software ForteBio N/A
ForteBio Data Acquisition v9 ForteBio N/A
Prism v8 GraphPad RRID:SCR_002798
FlowJo v10.8.0 FlowJo RRID:SCR_008520
UCSF Chimera v1.14 Pettersen et al., 2004 RRID:SCR_004097
HIV Databases (Los Alamos) http://www.hiv.lanl.gov/content/index RRID:SCR_000614
CATNAP https://www.hiv.lanl.gov/catnap RRID:SCR_016170
Leginon software package Suloway et al., 2005 RRID:SCR_016731
Appion package Lander et al., 2009 RRID:SCR_016734
R Package https://www.r-project.org/ RRID: SCR_001905
HD-Examiner Sierra Analytics N/A
HX-Express v2 Guttman et al., 2014, Weis et al., 2006 N/A
Other
Anti-human Fc capture (AHC) Biosensors ForteBio Cat# 18-5060
FEI Tecnai Spirit T12 transmission electron microscope Tecnai N/A
Synapt G2-Si Q-TOF mass spectrometer Waters N/A
Octet RED384 System ForteBio, Sartorius N/A
Carbon coated Cu400 grid for NS-EM Electron Microscopy Sciences Cat# EMS400-CU