Skip to main content
. 2022 Mar 7;11:e72416. doi: 10.7554/eLife.72416

Appendix 1—key resources table.

Reagent type (species) or resource Designation Source or reference Identifiers Additional information
Strain, strain background (E. coli) One shot Top10 Competent Cells Invitrogen C4040-06 Plasmid production
Cell line (Homo sapiens) FreeStyle 293 F cells Thermo Fisher Scientific R79007 Cell line for protein expression
Cell line (Homo sapiens) K-562 bone marrow chronic myelogenous leukemia (CML) cells ATCC ATCC CCL-243 Cell line for cell-aggregation assays
Transfected construct (M. musculus) α41–5 This paper Pcdhα4 EC1–5, Honig/Shapiro labs
Transfected construct (M. musculus) α71–5 Rubinstein et al., 2015
Transfected construct (M. musculus) α121–5 This paper Pcdhα12 EC1–5, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 Goodman et al., 2016c
Transfected construct (M. musculus) β81–4 Goodman et al., 2016c
Transfected construct (M. musculus) γA11–4 Goodman et al., 2016a
Transfected construct (M. musculus) γA41–4 Goodman et al., 2016a
Transfected construct (M. musculus) γA81–4 Rubinstein et al., 2015
Transfected construct (M. musculus) γA91–5 Goodman et al., 2016a
Transfected construct (M. musculus) γB21–5 Goodman et al., 2016a
Transfected construct (M. musculus) γB41–5 This paper PcdhγB4 EC1–5, Honig/Shapiro labs
Transfected construct (M. musculus) γB51–4 Goodman et al., 2016a
Transfected construct (M. musculus) αC21–4 Rubinstein et al., 2015
Transfected construct (M. musculus) γC31–4 Goodman et al., 2016a
Transfected construct (M. musculus) γC41–4 This paper PcdhγC4 EC1–4, Honig/Shapiro labs
TRansfected construct (M. musculus) γC51–5 Rubinstein et al., 2015
Transfected construct (M. musculus) α71–5-AVI This paper Biotinylated Pcdhα7 EC1–5, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4-AVI This paper Biotinylated Pcdhβ6 EC1–4, Honig/Shapiro labs
Transfected construct (M. musculus) β81–4-AVI This paper Biotinylated Pcdhβ8 EC1–4, Honig/Shapiro labs
Transfected construct (M. musculus) γA81–4-AVI This paper Biotinylated PcdhγA8 EC1–4, Honig/Shapiro labs
Transfected construct (M. musculus) γA91–5-AVI This paper Biotinylated PcdhγA9 EC1–5, Honig/Shapiro labs
Transfected construct (M. musculus) γB21–5-AVI This paper Biotinylated PcdhγB2 EC1–5, Honig/Shapiro labs
Transfected construct (M. musculus) αC21–4-AVI This paper Biotinylated PcdhαC2 EC1–4, Honig/Shapiro labs
Transfected construct (M. musculus) γC31–4-AVI This paper Biotinylated PcdhγC3 EC1–4, Honig/Shapiro labs
Transfected construct (M. musculus) γC41–4-AVI This paper Biotinylated PcdhγC4 EC1–4, Honig/Shapiro labs
Transfected construct (M. musculus) γC51–5-AVI This paper Biotinylated PcdhγC5 EC1–5, Honig/Shapiro labs
Transfected construct (M. musculus) α41–4-AVI This paper Biotinylated Pcdhα4 EC1–4, Honig/Shapiro labs
Transfected construct (M. musculus) α71–5 L301R This paper Pcdhα7 EC1–5 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γA81–4 I116R Rubinstein et al., 2015 PcdhγA8 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 R41N This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γC51–5 S116R This paper PcdhγC5 EC1–5 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 S117I This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 L125P This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 E369K This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 Y371F This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 R41N/S117I This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 R41N/E369K This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 S117I/L125P This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 R41N/S117I/L125P This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 R41N/S117I/E369K This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 R41N/S117I/Y371F This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β61–4 R41N/S117I/L125P/E369K/Y371F This paper Pcdhβ6 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γC41–4 E78A This paper PcdhγC4 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γC41–4 E78Q This paper PcdhγC4 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γC41–4 S344R This paper PcdhγC4 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γC41–4 D290A This paper PcdhγC4 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γC41–4 D290N This paper PcdhγC4 EC1–4 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) β13–6 This paper Pcdhβ1 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) β61–6 This paper Pcdhβ6 EC1–6, Honig/Shapiro labs
Transfected construct (M. musculus) β93–6 This paper Pcdhβ9 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) γA33–6 This paper PcdhγA3 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) γA43–6 Goodman et al., 2016a
Transfected construct (M. musculus) γA93–6 This paper PcdhγA9 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) γB23–6 Goodman et al., 2016a
Transfected construct (M. musculus) γB53–6 Goodman et al., 2016a
Transfected construct (M. musculus) γB73–6 Goodman et al., 2016a
Transfected construct (M. musculus) αC22–6 Goodman et al., 2016a
Transfected construct (M. musculus) α71–5/γC36 chimera Goodman et al., 2016a
Transfected construct (M. musculus) γC33–6 Goodman et al., 2016a
Transfected construct (M. musculus) γC52–6 This paper PcdhγC5 EC2–6, Honig/Shapiro labs
Transfected construct (M. musculus) β93–6-AVI This paper Biotinylated Pcdh β9 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) γA43–6-AVI This paper Biotinylated PcdhγA4 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) γA93–6-AVI This paper Biotinylated PcdhγA9 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) γB23–6-AVI This paper Biotinylated PcdhγB2 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) αC23–6-AVI This paper Biotinylated Pcdh αC2 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) γC33–6-AVI This paper Biotinylated PcdhγC3 EC3–6, Honig/Shapiro labs
Transfected construct (M. musculus) γC52–6-AVI This paper Biotinylated PcdhγC5 EC2–6, Honig/Shapiro labs
Transfected construct (M. musculus) γA43–6 V560R This paper PcdhγA4 EC3–6 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γC33–6 V560R This paper PcdhγC3 EC3–6 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γA43–6 K558R This paper PcdhγA4 EC3–6 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γC33–6 R558K This paper PcdhγC3 EC3-6 mutant, Honig/Shapiro labs
Transfected construct (M. musculus) γB73–6 Y532G Goodman et al., 2017
Transfected construct (M. musculus) γB73–6 A570R This paper PcdhγB7 EC3–6 mutant, Honig/Shapiro labs
Peptide, recombinant protein NeutrAvidin-HRP Thermo Fisher Scientific 31,030 Biotinylated protein western bot
Peptide, recombinant protein NeutrAvidin protein Thermo Fisher Scientific 31,000 SPR assays
Peptide, recombinant protein BSA Sigma-Aldrich A7906 SPR assays
Commercial assay or kit Spin Miniprep Kit Qiagen 27,106
Commercial assay or kit Hi-speed Plasmid Maxi Kit Qiagen 12,663
Commercial assay or kit SF Cell Line 4D-Nucleofector X Kit S Lonza V4XC-2032
Commercial assay or kit Amine-coupling kit Cytiva BR100050 SPR experiments
Commercial assay or kit Morpheus Amino Acids Molecular Dimensions MD2-100-77 Crystallography
Commercial assay or kit Morpheus Buffer System II Molecular Dimensions MD2-100-101 Crystallography
Chemical compound Polyethylenimine Polysciences 24765-2 Transfection
Chemical compound Biotin Sigma-Aldrich B4501 Protein biotinylation
Chemical compound Tris Base Fisher Scientific BP152-5
Chemical compound Sodium Chloride Fisher Scientific S271-10
Chemical compound Calcium Chloride Dihydrate JT Baker 1336-01
Chemical compound Imidazole ACROS 301870025
Chemical compound HEPES Sigma-Aldrich H3375
Chemical compound Tween-20 Sigma-Aldrich P7949
Chemical compound Sodium Acetate Sigma-Aldrich S7545
Chemical compound IMAC Sepharose 6 Fast Flow Cytiva 17092109
Chemical compound Penicillin Streptomycin Thermo Fisher Scientific 15070063
Chemical compound PEG 6000 Sigma-Aldrich 81,260
Chemical compound PEG 8000 Sigma-Aldrich 89,510
Chemical compound Ethylene Glycol Fluka 03760
Chemical compound Lithium Chloride Sigma-Aldrich L8895
Chemical compound MES Sigma-Aldrich M3671
Chemical compound Glycerol ACROS 332031000
Software, algorithm UCLA Diffraction Anisotropy Server Strong et al., 2006 https://srv.mbi.ucla.edu/Anisoscal/
Software, algorithm SednTerp Thomas Laue http://bitcwiki.sr.unh.edu/index.php/Main_Page
Software, algorithm HeteroAnalysis https://core.uconn.edu/auf
Software, algorithm Scrubber 2.0 BioLogic Software http://www.biologic.com.au
Software, algorithm Phaser McCoy et al., 2007 Implemented in CCP4 or Phenix (see below)
Software, algorithm CCP4 Winn et al., 2011 https://www.ccp4.ac.uk/
Software, algorithm Phenix Liebschner et al., 2019 http://www.hkl-xray.com/
Software, algorithm XDS Kabsch, 2010 http://xds.mpimf-heidelberg.mpg.de
Software, algorithm AIMLESS Evans and Murshudov, 2013 http://www.ccp4.ac.uk
Software, algorithm Coot Emsley et al., 2010 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Software, algorithm PISA Krissinel and Henrick, 2007 http://www.ebi.ac.uk/pdbe/protint/pistart.html
Software, algorithm Pymol Schrödinger https://pymol.org
Software, algorithm UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/
Software, algorithm Clustal Omega Sievers et al., 2011 https://www.ebi.ac.uk/Tools/msa/clustalo/
Software, algorithm WebLogo 3.0 Crooks et al., 2004 http://weblogo.threeplusone.com/
Software, algorithm SignalP 4.0 Petersen et al., 2011 https://services.healthtech.dtu.dk/service.php?SignalP-5.0
Software, algorithm ASTRA Wyatt https://www.wyatt.com/products/software/astra.html
Other Freestyle 23 Expression Media Thermo Fisher Scientific 12338-018 Protein expression media
Other Opti-MEM Reduced Serum Media Thermo Fisher Scientific 31985-070 Protein expression media
Other Series S CM4 chip Cytiva BR100539 SPR assays
Other Fetal Bovine Serum Thermo Fisher Scientific 16141079 Cell-aggregation assays media
Other DMEM with GlutaMAX Thermo Fisher Scientific 10569010 Cell-aggregation assays media