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. 2023 May 18;42(5):112524. doi: 10.1016/j.celrep.2023.112524
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

19.7E Robinson et al., 2016 Patent WO2018106712A1
12.1F Robinson et al., 2016 Patent WO2018106712A1
25.10C Robinson et al., 2016 Patent WO2018106712A1
37.7H Robinson et al., 2016 Patent WO2018106712A1
S370.7 This study N/A
StrepMAB-Classic Oyster 645 conjugate IBA Lifesciences Cat# 2-1555-050
Cy3 conjugated goat-anti-human Jackson Immuno Research Cat# 109-165-008; RRID: AB_2337720
Totalseq-C Anti-Human Hashtag #1 Biolegend Cat# 394661; RRID: AB_2801031
Totalseq-C Anti-Human Hashtag #2 Biolegend Cat# 394663; RRID: AB_2801032
Totalseq-C Anti-Human Hashtag #3 Biolegend Cat# 394665; RRID: 2801033
Totalseq-C Anti-Human Hashtag #4 Biolegend Cat# 394667; RRID: 2801034
APC-Cy7 Mouse Anti-Human CD3 BD Biosciences Cat# 557757; RRID: AB_396863
APC-Cy7 Mouse Anti-Human CD4 Biolegend Cat# 317418; RRID: AB_571947
APC-Cy7 Mouse Anti-Human CD8 BD Biosciences Cat# 557760; RRID: AB_396865
APC-H7 Mouse Anti-Human CD14 BD Biosciences Cat# 561384; RRID: AB_10611720
PerCP-Cy5.5 Mouse Anti-Human CD19 Biolegend Cat# 302230; RRID: AB_2073119

Bacterial and Virus Strains

NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat# C2987H
Lassa virus (Josiah strain) Brouwer et al., 2022 N/A

Biological Samples

Convalescent patient serum Robinson et al., 2016 N/A

Chemicals, Peptides, and Recombinant Proteins

Tween20 Sigma-Aldrich Cat# P1379-500ML
Bovine Serum Albumin (fraction V) Thermo Scientific Cat# 9048-46-8
Penicillin Sigma-Aldrich Cat# P3032-10MI
Streptomycin VWR Cat# 382-EU-100G
Iodacetamide Sigma-Aldrich Cat# I1149
BioLock solution IBA Lifesciences Cat# 2-0205-050
PBS Thermo Scientific Cat# 10010023
TBS Alfa Aesar Cat# J60764.K2
PEI MAX Polysciences Cat# 24765-1
Uranyl Formate Electron Microscopy Sciences Cat #D310 25 GM
Fluorinated octyl maltoside Anatrace Part# O310F
Imidazole Sigma-Aldrich Cat# I5513
Papain from papaya latex Sigma-Aldrich SKU# P4762
Acetonitrile, 80%, 20% Water with 0.1% Formic Acid, Optima LC/MS Fisher Scientific Cat# 15431423
Water with 0.1% Formic Acid (v/v), Optima™ LC/MS Grade Fisher Scientific Cat# LS118-212
Acetonitrile Fisher Scientific Cat# 10489553
Trifluoroacetic acid Fisher Scientific Cat# 10155347
Dithiothreitol Sigma-Aldrich Cat# 43819
Mass spectrometry grade trypsin Promega Cat# V5280
Sequencing grade chymotrypsin Promega Cat# V1061
α-Lytic Protease New England Biolabs Cat# P8113L
Urea Sigma-Aldrich U5378-1KG
Fugene Promega Cat# E5911
DEAE-dextran Sigma-Aldrich Cat# D9885
Saquinavir NIH-ARP Cat# 4658
Reporter Lysis buffer Promega Cat# E3971
Fetal Bovine Serum Omega Scientific, Inc. FB-02
RPMI 1640 Corning 15-040-CV
Trypan Blue Sigma-Aldrich T8154-100ML
Ethanol Pharmaco 111000200
FectoPRO Polyplus Transfection 101000019
Citric acid Fisher Scientific BP339-500
Tris Base Sigma-Aldrich T1503-5KG

Critical Commercial Assays

Bright-Glo Luciferase Assay System Promega Cat# E2620

Deposited Data

3D map of LIV GPC-I53-50A (strain Josiah) This study EMDB: EMD-28178
3D model of LIV GPC-I53-50A (strain Josiah) This study PDB: 8EJD
3D map of LII GPC-I53-50A (strain NIG08-A41) This study EMDB: EMD-28179
3D model of LII GPC-I53-50A (strain NIG08-A41) This study PDB: 8EJE
3D map of LV GPC-I53-50A (strain Soromba-R) This study EMDB: EMD-28180
3D model of LV GPC-I53-50A (strain Soromba-R) This study PDB: 8EJF
3D map of LVII GPC-I53-50A (strain Soromba-R) This study EMDB: EMD-28181
3D model of LVII GPC-I53-50A (strain Soromba-R) This study PDB: 8EJG
3D map of LIV GPC-I53-50A (strain Josiah_ bound to 12.1F Fab This study EMDB: EMD-28182
3D model of LIV GPC-I53-50A (strain Josiah_ bound to 12.1F Fab This study PDB: 8EJH
3D map of LIV GPC-I53-50A (strain Josiah_ bound to 19.7E Fab This study EMDB: EMD-28183
3D model of LIV GPC-I53-50A (strain Josiah_ bound to 19.7E Fab This study PDB: 8EJI
3D map of LIV GPC-I53-50A (strain Josiah_ bound to S370.7 Fab This study EMDB: EMD-28184
3D model of LIV GPC-I53-50A (strain Josiah_ bound to S370.7 Fab This study PDB: 8EJJ
Mass spectrometry data This study ftp://massive.ucsd.edu/MSV000091003/
S370.7 HC sequence This study GenBank: OQ451467
S370.7 LC sequence This study GenBank: OQ451468

Experimental Models: Cell Lines

FreeStyle 293F cells Thermo Scientific Cat# R79007
HEK 293T cells ATCC Cat# CRL-11268
Expi293T cells ATCC CRL-3216
TZM-bl cells NIH ARRRP Cat# 8129

Experimental Models: Organisms/Strains

Recombinant DNA

GPCysR4(Josiah)-StreptagII pPPI4 plasmid Brouwer et al., 2022 N/A
GPCysR4(Josiah)-I53-50A.1NT1-Strep-tagII pPPI4 plasmid Brouwer et al., 2022 N/A
GPCysR4(NIG08-A41)-I53-50A.1NT1-Strep-tagII pPPI4 plasmid This study N/A
GPCysR4(Soromba-R)-I53-50A.1NT1-Strep-tagII pPPI4 plasmid This study N/A
GPCysR4(Togo)-I53-50A.1NT1-Strep-tagII pPPI4 plasmid This study N/A
GPCysR4(Josiah)-I53-50A.1NT1-Avi-His pPPI4 plasmid Brouwer et al., 2022 N/A
GPCysR4(NIG08-A41)-I53-50A.1NT1-Avi-His pPPI4 plasmid Brouwer et al., 2022 N/A
GPCysR4(Soromba-R)-I53-50A.1NT1-Avi-His pPPI4 plasmid This study N/A
GPCysR4(Togo)-I53-50A.1NT1-Avi-His pPPI4 plasmid This study N/A
GPCysR4(Soromba-R_D114N)-I53-50A.1NT1-StrepTagII pPPI4 plasmid This study N/A
Furin pPPI4 plasmid Brouwer et al., 2019 N/A
S1P pcDNA3.0 plasmid This study N/A
GPCysRRLL(Josiah)-I53-50A.1NT1-Strep-tagII pPPI4 plasmid This study N/A
Fc-tagged LAMP-1 ectodomain Jae et al., 2014 N/A
GPC(NIG08-A41)_full-length pPPI4 plasmid Brouwer et al., 2022 N/A
GPC(Josiah)_full-length pPPI4 plasmid Brouwer et al., 2022 N/A
GPC(CSF)_full-length pPPI4 plasmid Brouwer et al., 2022 N/A
19.7E HC, 19.7E LC, 12.1F HC, 12.1F LC, 25.10C HC, 25.10C LC, 37.7H HC, 37.7H LC gene fragments Integrated DNA Technologies N/A
S370.7 HC and LC gene fragments This study N/A

Software and Algorithms

GraphPad Prism v8 GraphPad N/A
UCSF Chimera Pettersen et al., 2004 N/A
UCSF ChimeraX Goddard et al., 2018 N/A
cryoSPARC.v3 Punjani et al., 2017 N/A
Leginon Suloway et al., 2005 N/A
MotionCor2 Zheng et al., 2017 N/A
GCTF Zhang, 2016 N/A
Relion/3.0 and 3.1 Zivanov et al., 2018 N/A
ABodyBuilder Leem et al., 2016 N/A
Coot Casañal et al., 2020 N/A
Phenix Liebschner, et al., 2019 N/A
EMRinger Barad et al., 2015 N/A
MolProbity Williams et al., 2018 N/A
Appion Lander et al., 2009 N/A
Epitope-Analyzer Montiel-Garcia, et al., 2022 N/A
PDBePISA Krissinel et al., 2007 N/A
Privateer Agirre et al., 2015 N/A
Byos™ (Version 4.0) Protein Metrics Inc. N/A
XCalibur Version v4.2 Thermo Fisher N/A
Orbitrap Fusion Tune application v3.1 Thermo Fisher N/A
Cellranger 6.0.2 10X Genomics N/A
ab[x] toolkit Briney et al., 2018 N/A
Single Cell Analysis of B cells (SCAB) Hurtado et al., 2022 N/A
GenePix Pro 7 software v7.2.29.2 Molecular Devices N/A

Other

PstI-HF New England Biolabs Cat# R3140S
BamHI-HF New England Biolabs Cat# R3136S
NotI-HF New England Biolabs Cat# R3189
Q5 Site-directed mutagenesis kit New England Biolabs Cat# E0554S
T4 DNA ligase New England Biolabs Cat# M0202
Quick ligation kit New England Biolabs Cat# M2200
Superdex200 10/300GL Column GE Healthcare Life Sciences Cat# 28990944
Protein G resin Cytiva Cat# 17061802
CaptureSelect IgG-Fc resin Thermo Scientific Cat# 2942852010
Ni-NTA agarose QIAGEN Cat# 30210
Amicon® Ultra-4 Centrifugal Filter Unit (100 kDA MWCO) Millipore Sigma SKU# UFC810024
Amicon® Ultra-4 Centrifugal Filter Unit (30 kDA MWCO) Millipore Sigma SKU# UFC803024
Amicon® Ultra-4 Centrifugal Filter Unit (10 kDA MWCO) Millipore Sigma SKU# UFC801024
Amicon Ultra-0.5 Centrifugal Filter Unit (100 kDa MWCO) Millipore Sigma SKU# UFC5100BK
Amicon Ultra-0.5 Centrifugal Filter Unit (30 kDa MWCO) Millipore Sigma SKU # UFC5030BK
Amicon Ultra-0.5 Centrifugal Filter Unit (10 kDA MWCO) Millipore Sigma SKU# UFC5010BK
Prometheus NT.Plex nanoDSF Grade High Sensitivity Capillary Chips Nanotemper Cat# PR-AC006
400-mesh copper grids Electron Microscopy Sciences Cat# 0400-Cu
Octet Red96 system Sartorius (FortéBio) N/A
Octet Biosensors: Streptavidin (SA) Sartorius (FortéBio) Cat# 18-5019
Octet Biosensors: Anti-Human Fc Capture (AHC) Sartorius (FortéBio) Cat# 18-5060
FreeStyle 293 Expression medium Thermo Scientific Cat# 12338018
OptiMEM Gibco Cat# 31985-070
DMEM Gibco Cat# 21969-035
Fetal calf serum Gibco Cat# 10270/106
BioLock IBA Lifesciences Cat# 2-0205-250
BXT Buffer (10X) IBA Lifesciences Cat# 2-1042-025
Steritop Filter Units Merck Millipore Cat# C3239
Greiner CELLSTAR® 96 well plates round bottom clear wells Merck Millipore Cat# M9436
Totalseq-C0951 PE-Streptavidin Biolegend Cat# 405183
Totalseq-C0992 PE-Streptavidin Biolegend Cat# 405181
Totalseq-C0994 PE-Streptavidin Biolegend Cat# 405177
Totalseq-C0956 APC-Streptavidin Biolegend Cat# 405261
Totalseq-C0958 APC-Streptavidin Biolegend Cat# 405293
Totalseq-C0971 Streptavidin Biolegend Cat# 405271
Totalseq-C0972 Streptavidin Biolegend Cat# 405273
Totalseq-C0973 Streptavidin Biolegend Cat# 405275
LIVE/DEAD Fixable Aqua Dead Cell Stain Kit Thermo Scientific Cat# L34966
Biotinylated Human Serum Albumin Protein Acro Biosystems Cat# HSA-H82E3
Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN# 1000287
Chromium Single Cell V(D)J Amplification Kit, Human BCR 10X Genomics PN# 1000255
Chromium 5’ Feature Barcode Kit 10X Genomics PN# 1000256
Chromium Next GEM Single Cell 5’ Gel Bead Kit v3 10X Genomics PN# 1000264
Chromium Next GEM Single Cell 5’ Library Construction Kit 10X Genomics PN# 1000190
96-well Skirted PCR plates White Barcoded Bio-Rad Cat# HSP9901
FACSMelody Cell sorter BD Biosciences N/A
Chromium Controller 10X Genomics N/A
NEBuilder HiFi DNA Assembly Master Mix New England Biolabs E2621X
NovaSeq 6000 Sequencing System Illumina N/A
NovaSeq 6000 S4 Reagent Kit v1.5 Illumina 20028313
NovaSeq 6000 S2 Reagent Kit v1.5 Illumina 20028316
NovaSeq 6000 S1 Reagent Kit v1.5 Illumina 20028319
NovaSeq 6000 SP Reagent Kit v1.5 Illumina 20028401
Glomax reader Turner BioSystems Model# 9101-002
UltrAuFoil R 1.2/1.3 grids (300-mesh) Quantifoil Micro Tools GmbH N/A
Strep-TactinXT Superflow high capacity resin IBA Life Sciences Cat# 2-4010-010
NanoDrop 2000C Thermo Scientific Cat# ND-2000C
Prometheus NT.48 NanoDSF NanoTemper Technologies N/A
Leica DMi1 Inverted Microscope Leica Microsystems N/A
Tecnai F20 electron microscope FEI N/A
TemCam F415 CMOS camera TVIPS N/A
Vitrobot mark IV Thermo Scientific N/A
Solarus 950 plasma system Gatan N/A
PELCO easiGlow Ted Pella Inc. N/A
Talos Arctica Thermo Scientific
FEI Titan Krios Thermo Scientific N/A
K2 Summit direct electron detector camera Gatan N/A
C18 ZipTip Merck Milipore Cat# ZTC18S008
Vivaspin 500, 3 kDa MWCO, Polyethersulfone Sigma-Aldrich Cat# GE28-9322-18
Orbitrap Eclipse mass spectrometer Thermo Fisher Scientific N/A
Ultimate 3000 HPLC Thermo Fisher Scientific N/A
EasySpray PepMap RSLC C18 column (75 μm x 75 cm) Thermo Fisher Scientific Cat# ES805
PepMap 100 C18 3μM 75μM x 2cm Thermo Fisher Scientific Cat# 164946
NEXTERION Slide H NHS-ester activated glass slides Schott Inc. SKU:1070936
sciFLEXARRAYER S3 non-contact microarray Scienion Inc. N/A
Scienion PDC80 nozzle Scienion Inc. N/A
GenePix 4000B microarray scanner Molecular Devices N/A