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. 2021 Jul 1;29(7):694–708.e7. doi: 10.1016/j.str.2020.12.012
REAGENT or RESOURCE SOURCE IDENTIFIER
Chemicals, peptides, and recombinant proteins
Gibco ™ Sf-900-III SFM Thermo Fisher Cat# 12658019
Lactalbumin Sigma Aldrich Cat# 58901C-100ML
Yeastolate Sigma Aldrich Cat# 58902C
Ex-Cell420 media Sigma Aldrich Cat# 14420C-1000ML
Fetal Bovine Serum Thermo Fisher Cat# 10082147
ExpreS2-Insect TR Expression Systems Cat# 95-055-075
Gibco ™ FreeStyle™ 293 Expression Medium Thermo Fisher Cat# 12338026
Polyethylimine Polysciences Cat# 19850
Optimem Thermo Fisher Cat# 31985062
FuGENE® HD Transfection Reagent Promega Cat# E2311
FlashBAC Gold Baculovirus Expression System 2B Scientific Cat# GWB-67B0AE
Glutaraldehyde (50 % v/v) Sigma Aldrich Cat# 49628
Recombinant protein: zebrafish RET (aa 1-504, ref# A8E7C6) This paper N/A
Recombinant protein: zebrafish RET (aa 1-626, ref# A8E7C6) This paper N/A
Recombinant protein: zebrafish GFRα1a (aa 1-353, ref# Q98TT9) This paper N/A
Recombinant protein: zebrafish GDNF (aa 135-235, ref# Q98TU0) This paper N/A
Recombinant protein: human RET (aa 1-635, ref# P07949) This paper N/A
Recombinant protein: human GFRAL (aa ref# Q6UXV0) This paper N/A
Recombinant protein: human GDF15 (aa ref# Q99988) This paper N/A
Critical commercial assays
Monolith Protein Labeling RED-NHS 2nd generation (Amine Reactive) Nanotemper Cat# MO-L001
Nanotemper hydrophobic capillaries Nanotemper Cat# MO-KO23
Deposited data
zRETCLD1-4 crystal structure This paper PDB: 7AMK
zGFRα1150-353-zGDNF135-235 complex crystal structure This paper PDB: 7AB8
zRET22-595- zGFRα129-353-zGDNF135-235 complex cryo-EM structure This paper PDB: 7AML
The zRGα1a C2 symmetry / the zRGα1a symmetry expanded cryo-EM maps This paper EMD11822
The hR15AL negative stain EM map This paper EMD11777
hRETCLD1-2 crystal structure Kjær et al., 2010 PDB: 2X2U
hRETECD-GDF15mat.GFRAL129-318 cryo-EM structure Li et al., 2019 PDB: 6Q2J
hGDNF-hGFRα1D2-D3 crystal structure Parkash and Goldman (2009) PDB: 3FUB
hGFRα2-neurturin crystal structure Sandmark et al., 2018 PDB: 5MR4
hRETECD-GFRα2-neurturin cryo-EM structure Li et al., 2019 PDB: 6Q2O
C-cadherin ectodomain crystal structure Boggon et al., 2002 PDB: 1L3W
N-cadherin EC1 domain crystal structure Shapiro et al., 1995 PDB: 1NCI
N-cadherin EC1 domain solution structure Koch et al., 2004 PDB: 1OP4
Protocadherin Beta 1 EC1-3 crystal structure Rubinstein et al., 2015 PDB: 4ZPL
Protocadherin Alpha C2 EC1-3 crystal structure Rubinstein et al., 2015 PDB: 4ZPM
Protocadherin Gamma C5 EC1-3 crystal structure Rubinstein et al., 2015 PDB: 4ZPO
Protocadherin Gamma A8 EC1-3 crystal structure Rubinstein et al., 2015 PDB: 4ZPS
E-cadherin domains 1 and 2 Nagar et al., 1996 PDB: 1EDH
Experimental models: cell lines
Human: Expi293 cells Thermo Fisher Cat# A14527
Insect: Sf21 cells Thermo Fisher Cat# 11497013
Insect: Hi Five cells Thermo Fisher Cat# B85502
Insect: Drosophila S2 cells Thermo Fisher Cat# R69007
Recombinant DNA
Plasmid: pCEP Kohfeldt et al., 1997 N/A
Plasmid: pCEP-hGFRAL-Histag This paper N/A
Plasmid: pCEP-hGDF15-Histag This paper N/A
Plasmid: pExpreS2.1 Expres2ion Biotech Cat# S2-11A-001
Plasmid: pExpreS2.1-hRET1-635-Tev-Avi-Ctag This paper N/A
Plasmid: pBacPak Clontech Laboratories, Inc. Cat# 631410
Plasmid: pBacPak-Mellitin1-20-zGDNF135-235 This paper N/A
Plasmid: pBacPak-zGFRα1a1-35n3-3C-Tev-ProteinA This paper N/A
Plasmid: pBacPak-zRET1-619-3C-TEV-ProteinA This paper N/A
Plasmid: pBacPak-zRET1-504(N259Q, N308Q, N309Q, N433Q) -3C-TEV-ProteinA This paper N/A
Software and algorithms
NanoTemper analysis software NanoTemper v1.2.231
GraphPad Prism GraphPad Software Inc. http://www.graphpad.com/scientific-software/prism/
DIALS Waterman et al., 2016, Winter et al., 2018 https://dials.github.io/
iMosflm & SCALA Winn et al., 2011 www.ccp4.ac.uk/
PHASER McCoy et al., 2007 http://www.phaser.cimr.cam.ac.uk/
PHENIX Adams et al., 2010 http://www.phenix-online.org/
Coot Emsley et al., 2010 http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/
RELION Scheres, 2012, Kimanius et al., 2016, Zivanov et al., 2018 https://github.com/3dem/relion
Scipion de la Rosa-Trevín et al., 2016 http://scipion.i2pc.es/
Xmipp de la Rosa-Trevín et al., 2013 http://scipion.i2pc.es/
Gautomatch K. Zhang, MRC LMB https://www.lmb.cam.ac.uk/kzhang/
CryoSparc Structa Biotechnology Inc. Punjani et al., 2017 https://cryosparc.com/
3DFSC Tan et al., 2017 https://3dfsc.salk.edu/, https://github.com/LyumkisLab/3DFSC
PyMOL DeLano Scientific LLC http://www.pymol.org/
Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/
Proteome Discoverer v.2.3 with XlinkX node Thermo Fisher, Liu et al., 2015, Kao et al., 2011 Cat# OPTON-30795/30799
xiNET Combe et al., 2015 Crosslinkviewer.org