Antibodies |
Flag 1:1,000 |
Sigma |
V8137 |
SPRED1 1:1,000 |
Cell Signaling |
94063 |
α/β-Tubulin 1:2,000 |
Cell Signaling |
2148 |
EGFR 1:200 |
Santa Cruz Biotech |
1005, SC-03 |
Neurofibromin 1:200 |
Santa Cruz Biotech |
SC-67 |
RAS 1:200 |
Cytoskeleton |
AESA02 |
β-Actin 1:10,000 |
Sigma-Aldrich |
A5441 |
Bacterial and Virus Strains |
BL21 STAR (DE3) |
Thermo Fisher |
C601003 |
Tni-FNL insect cells |
FNLCR |
Tni-FNL |
Baculovirus, Bac-to-Bac |
Thermo Fisher |
AcMNPV |
Retrovirus: pMD2.G |
Addgene |
12259 |
Retrovirus: gag/pol |
Addgene |
14887 |
Biological Samples |
HEK293T |
UCSF Cell and Genome Engineering Core |
CCLZR076 |
K562 |
UCSF Cell and Genome Engineering Core |
CCLZR466 |
Chemicals, Peptides, and Recombinant Proteins |
protease inhibitor (PI) cocktail |
Sigma-Aldrich |
P8849, P8340 |
ANAPOE®-80 |
Molecular Dimensions |
APT080 500 ML |
PGA-LM |
Molecular Dimensions |
MD2-250-108 |
PEG3350 (50% w/v) |
Hampton Research |
HR2-527 |
DMEM, high glucose |
Thermo Fisher |
11965-084 |
RPMI 1640 |
Thermo Fisher |
118775-093 |
FBS |
Atlanta Biologicals |
S11550H |
Penicillin-Streptomycin |
Thermo Fisher |
15140-122 |
Opti-MEM Reduced Serum Medium |
Thermo Fisher |
51985091 |
phosphatase inhibitors |
Sigma Aldrich |
P0044, P5726 |
EGF |
Thermo Fisher |
PHG0311 |
Nuclear and Cytoplasmic Extraction Reagents |
Thermo Fisher |
78835 |
Lipofectamine 3000 Transfection Reagent |
Thermo Fisher |
L3000015 |
ViralBoost Reagent |
Alstem |
VB1000 |
trypsin |
Sigma Trypsin Singles |
T7575 |
Critical Commercial Assays |
RAS Pull-down Activation Assay Biochem Kit |
Cytoskeleton |
BK008 |
Lipofectamine 2000 Transfection Reagent |
Thermo Fisher |
11668019 |
Deposited Data |
Crystal structure of KRAS-NF1-SPRED1 |
This study |
PDB:6V65 |
Crystal structure of KRAS(Q61L)-NF1-SPRED1 |
This study |
PDB:6V6F |
Experimental Models: Cell Lines |
HEK293T |
UCSF Cell and Genome Engineering Core |
CCLZR076 |
K562 |
UCSF Cell and Genome Engineering Core |
CCLZR466 |
Spred1(S105A)-Forward PrimerGGTCTTACGTTTCAAGCTCCTGCTGATGCTAGG |
Sigma-Aldrich |
N/A |
Spred1(S105A)-Reverse PrimerCCTAGCATCAGCAGGAGCTTGAAACGTAAGACC |
Sigma-Aldrich |
N/A |
Spred1(S105D)-Forward PrimerGTTTGGTCTTACGTTTCAACATCCTGCTGATGCTAGGGC |
Sigma-Aldrich |
N/A |
Spred1(S105D)-Reverse PrimerGCCCTAGCATCAGCAGGATGTTGAAACGTAAGACCAAAC |
Sigma-Aldrich |
N/A |
Spred1(S105E)-Forward PrimerGGTCTTACGTTTCAAGAACCTGCTGATGCTAG |
Sigma-Aldrich |
N/A |
Spred1(S105E)-Reverse PrimerCTAGCATCAGCAGGTTCTTGAAACGTAAGACC |
Sigma-Aldrich |
N/A |
Spred1(W31C)-Forward PrimerCTCAAGTGGTGGATGCTTACCACTTGGAGGG |
Sigma-Aldrich |
N/A |
Spred1(W31C)-Reverse PrimerCCCTCCAAGTGGTAAGCATCCACCACTTGAG |
Sigma-Aldrich |
N/A |
Spred1(T102R)-Forward PrimerCAAGAAGTTTGGTCTTAGGTTTCAAAGTCCTGCTG |
Sigma-Aldrich |
N/A |
Spred1(T102R)-Reverse PrimerCAGCAGGACTTTGAAACCTAAGACCAAACTTCTTG |
Sigma-Aldrich |
N/A |
Recombinant DNA |
pDZ2087 (Expresses TEV protease in E. coli) |
Addgene |
92414 |
pMIG |
Addgene |
9044 |
pMD2.G |
Addgene |
12259 |
SPRED1 expression plasmid for cellular assay |
(Stowe et al., 2012) |
N/A |
Software and Algorithms |
XDS |
(Kabsch, 2010) |
N/A |
Phaser |
(McCoy et al., 2007) |
N/A |
Phenix |
(Adams et al., 2010) |
N/A |
COOT |
(Emsley et al., 2010) |
N/A |
DSSP |
https://swift.cmbi.umcn.nl/gv/dssp/). |
N/A |
PyMOL |
Schrödinger, LLC |
Ver: 2.3.2 |
SBGrid Consortium |
(Morin et al., 2013) |
N/A |
PDBSum |
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html/ |
N/A |
MicroCal PEAQ-ITC analysis software |
Malvern |
N/A |
Proteome Discoverer |
Thermo Fisher |
Ver: 1.4 |
Protein Prospector |
(Baker and Chalkley, 2014; Chalkley et al., 2005) |
Ver: 5.14.0 |
SwissProt database |
(Bairoch and Apweiler, 2000) |
N/A |
Skyline v 3.0 |
(MacLean et al., 2010) |
V 3.0 |
Other |
Immobilized metal affinity chromatography columns |
GE Healthcare |
18-1174-40 |
NGC chromatography system |
Bio-Rad Laboratories |
NGC-100 |
10K MWCO Amicon centrifugation units |
MilliporeSigma |
UFC901008 |
MicroCal PEAQ-ITC |
Malvern |
N/A |
Anti-FLAG antibodies coupled to magnetic beads |
Sigma |
M8823 |
Liquid chromatography tandem mass spectrometry |
Thermo Fisher |
N/A |
Silica-C18 EasySpray column |
Thermo Fisher |
N/A |