REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
penta-His primary antibody | QIAGEN | cat#34660; RRID: AB_2619735 |
Horse radish peroxidase-linked secondary antibody | Thermo Fisher Scientific | cat# 32230; RRID: AB_1965958 |
FLAG monoclonal antibody | Cell Signaling | 3916S; RRID: AB_10694611 |
Mouse monoclonal anti rat CD4 (clone OX-68) (for AVEXIS prey and bait protein normalization) | Bio-Rad/AbD Serotec | MCA1022R; RRID: AB_567282 |
Chemicals, Peptides, and Recombinant Proteins | ||
Draxin peptide: GEVMPTLDMALFDWTDYEDLKP | Genscript | hDraxin-22 |
Nitrocefin CAS 41906-86-9 | Merck | Cat# 484400 |
Deposited Data | ||
Crystal Structure of rDraxin/ rDCCIg1-Ig4 complex | This study | PDB: 5Z5K |
Crystal structure of hNetrin-1/hDraxin-22 complex | This study | PDB: 6FKQ |
SAXS experimental data | This study | SASBDB: SASDBZ6 |
Experimental Models: Cell Lines | ||
HEK293T cells | ATCC | CRL-11268 |
COS Cells | ATCC | CRL-1651 |
FreeStyle 293-F Cells | Thermo Fisher Scientific | R79007 |
Oligonucleotides | ||
5′ ATTTA GCGGCCGCC ATGGCAGGGTCCGTC 3′ | This study | rat Draxin forward primer signal sequence. |
5′ GCCCC GAGCTC GATGTTGATGAAAGATCCC 3′ | This study | rat Draxin, reverse primer |
5′ TGGAGCCACCCCCAGTTCGAGAAGGGCGGCT CTCTTCATTTTGTGTCTGAACC 3′ |
This study | rat DCC (residues 39-422) forward primer |
5′ TTAAA GGTACC GGCGGCTGGAGCCACCCC CAG 3′ |
This study | rat DCC reverse primer |
5′ AATAT GAGCTC GATGGCAGGCTTGGGG 3′ | This study | rat DCC reverse primer |
5′ GCGGCCGCCACC ATGGCTGGGCCTGCCATC CACACCGCTC 3′ |
(Gao et al., 2015) | human Draxin forward primer with signal sequence |
5′ GGCGCGCC GACGTTGATGAAGGATCCCT GGTC 3′ |
(Gao et al., 2015) | human Draxin full length reverse primer |
5′ ATAAGAAT GCGGCCGC CATGGGAACCCTC 3′ | This study | common primer from pXLG to AVEXIS vector, forward primer |
5′ A GGCGCGCC ATGGTGGTGGTGGTGGTG GAGCTC 3′ |
This study | common primer from pXLG to AVEXIS vector, reverse primer |
Recombinant DNA | ||
Plasmid: pXLG-rDraxin | This study | N/A |
Plasmid: pXLG-hNetrin-1 | (Finci et al., 2014) | N/A |
Plasmid: rDCC Ig1-Ig4 | (Chen et al., 2013) | N/A |
Plasmid: AVEXIS-hDraxin-prey | (Gao et al., 2015) | Addgene #36148 |
Plasmid: AVEXIS-hDraxin-bait | (Gao et al., 2015) | Addgene #36149 |
Software and Algorithms | ||
HKL2000 | (Otwinowski and Minor, 1997) | N/A |
Phaser | (Bunkóczi et al., 2013) | N/A |
Coot | (Emsley et al., 2010) | N/A |
Phenix | (Afonine et al., 2012) | N/A |
Molprobity | (Chen et al., 2010) | N/A |
Pymol | The PyMOL Molecular Graphics System, Version 1.7.x Schrödinger, LLC | N/A |
ESPRIPT | (Robert and Gouet, 2014) | N/A |
MOSFLM | (Battye et al., 2011) | N/A |
SCALA | (Evans, 2006) | N/A |
MOLREP | (Vagin and Teplyakov, 2010) | N/A |
REFMAC5 | (Murshudov et al., 2011) | N/A |
CCP4 Suite | (Winn et al., 2011) | N/A |
Prism | GraphPad | N/A |
RADAVER | Franke et al. (2012) | https://www.embl-hamburg.de/biosaxs/download.html |
PRIMUS/Qt | Petoukhov et al. (2012) | https://www.embl-hamburg.de/biosaxs/download.html |
CRYSOL | Petoukhov et al. (2012) | https://www.embl-hamburg.de/biosaxs/download.html |
DAMMIF | Franke and Svergun, 2009 | https://www.embl-hamburg.de/biosaxs/download.html |
SASVIEW | NSF DANSE | http://www.sasview.org |
Other | ||
Mutagenesis kit | Agilent Techologies | #200521 |
Dulbecco’s modified eagle medium | DMEM, Biochrom | cat# F 0435 |
L-glutamine | Biochrom | cat# K 0293 |
fetal-bovine serum | Biochrom | cat# S 0615 |
Protease Inhibitor Cocktail tablets | cOmplete ULTRA Tablets, Roche | 05892791001 |
Ni-Sepharose Excel resin | GE Healthcare | cat# 17-3712-02 |
HiLoad 16/60 Superdex 75 column | GE Healthcare | #28-9893-33 |
Nickel-NTA agarose beads | QIAGEN | Cat No./ID: 30250 |