| Antibodies |
| LM609 |
Sigma Aldrich |
MAB1976 |
| APC-labeled goat anti-mouse Fc-specific antibody |
Jackson ImmunoResearch |
115–055–008 |
|
|
|
| Bacterial and Virus Strains |
| BacMagic baculovirus DNA (derived from AvNPV genome) |
Novagen |
72350–3 |
| Bl21-DE3 |
New England Biolabs |
C2527 |
|
|
|
| Chemicals, Peptides, and Recombinant Proteins |
| Peptide 2.5F |
(Kimura et al., 2009b) |
N/A |
| Peptide 2.5D |
(Kimura et al., 2009b) |
N/A |
| KpnI |
New England Biolabs |
R0142M |
| BamhI |
New England Biolabs |
R0136M |
| EcoRI |
New England Biolabs |
R0101M |
| BssHII |
New England Biolabs |
R0199M |
| XbaI |
New England Biolabs |
R0145M |
| Penicillin-Streptomycin |
ThermoFisher |
15140122 |
| PBS |
Boston BioProducts |
Cat#BM-220 |
| Hepes |
Boston BioProducts |
Cat#BBH-85 |
| Alexa Fluor 647 dye |
Invitrogen Corp (San Diego) |
Cat#A20173 |
| Alexa Fluor 488 dye |
Invitrogen Corp (San Diego) |
Cat#A10235 |
| Dulbecco’s Modified Eagle Medium (DMEM) |
Invitrogen |
Cat#11965126 |
| Iscove’s Modified Dulbecco’s Medium (IMDM) |
Invitrogen |
Cat#12440061 |
| Dulbecco’s Phosphate Buffer Saline (DPBS) |
|
Cat#A1285801 |
| Fetal Bovine Serum (FBS) |
Invitrogen |
Cat#16000036 |
| Cell Dissociation Buffer, Enzyme Free PBS |
Invitrogen |
Cat#13151013 |
| Lipofectamine 2000 |
Invitrogen |
Cat#11668027 |
| Ni-NTA agarose |
Qiagen |
Cat#30210 |
| Protein A Sepharose |
Sigma |
Cat#P3391 |
| Tris |
Sigma |
Cat#252859 |
| MgCl2
|
Sigma |
Cat#M8266 |
| CaCl2
|
Sigma |
Cat#449709 |
| MnCl2
|
Sigma |
Cat#244589 |
| L-glutamine |
Invitrogen |
Cat#21051024 |
| Penicillin/Streptavidin |
Invitrogen |
Cat#15140122 |
| IPTG |
Sigma |
Cat#6758 |
| Bovine Serum Albumin |
Sigma |
Cat#A2058 |
| Critical Commercial Assays |
| QuikChange Lightning |
Agilent |
Cat#210515 |
|
| Deposited Data |
|
|
| 2.5F (apo) structure |
This paper |
PDB: 6MM4 |
| 2.5D (apo) structure |
(Kryshtafovych et al., 2014) |
PDB: 2M7T |
| 2.5F-αVβ3 structure |
This paper |
PDB: 6MSL |
| 2.5D-αVβ3 structure |
This paper |
PDB: 6MSU |
|
| Experimental Models: Cell Lines |
|
|
| U87MG glioblastoma cells |
ATCC (Manassas, VA) |
Cat#HTB-14 |
| K562 leukemia cells |
Blystone et. al, 1994 |
SUNY Upstate Medical University |
| HEK293T |
ATCC (Manassas, VA) |
Cat#CRL-3216 |
|
| Oligonucleotides |
|
|
| β3-M180A-F gaaaacccctgctatgatgcgaagaccacctgcttgcc |
This paper |
N/A |
| β3-M180A-R ggcaagcaggtggtcttcgcatcatagcaggggttttc |
This paper |
N/A |
| β3-R214G-F gtgaagaagcagagtgtgtcacggaaccgagat |
This paper |
N/A |
| β3-R214G-R atctcggttccgtgacacactctgcttcttcac |
This paper |
N/A |
|
| Recombinant DNA |
|
|
| pcDNA3-αV |
(Gupta et al., 2007) |
N/A |
| pcDNA3-β3 |
(Gupta et al., 2007) |
N/A |
| pBacPAK8-αV |
(Mehta et al., 1998) |
N/A |
| pBacPAK8-β3 |
(Mehta et al., 1998) |
N/A |
| pET-32–2.5d |
(Kryshtafovych et al., 2014) |
N/A |
| pET-32–2.5F |
This paper |
N/A |
| pADD2 shuttle vector |
(Moore et al., 2013) |
N/A |
|
| Software and Algorithms |
|
|
| SigmaPlot |
Systat software |
https://systatsoftware.com |
| FlowJo |
TreeStar Inc. |
https://www.flowjo.com |
| HKL2000 |
(Otwinowski and Minor, 1997) |
http://www.hklxray.com |
| Phaser |
|
https://www.phenix-online.org |
| Coot |
(Emsley and Cowtan, 2004) |
https://www2.mrclmb.cam.ac.uk/personal/pemsley/coot/ |
| Phenix |
(Adams et al., 2010) |
https://www.phenix-online.org |
| PyMol |
Schrödinger |
https://pymol.org/2/ |
| Haddock |
|
http://www.bonvinlab.org/software/haddock2.2/ |
| Charmm27 |
(Brooks et al., 2009) |
https://www.charmm.org/charmm/?CFID=a0742b750ba2–4feb-94e3a1fc7391a45a&CFTOKEN=0 |
| NAMD |
(Phillips et al., 2005) |
http://www.ks.uiuc.edu/Research/namd/ |
| VMD |
(Humphrey et al., 1996) |
http://www.ks.uiuc.edu/Research/vmd/ |
| CYANA |
(Guntert et al., 1997) |
http://www.cyana.org |
| YASARA |
|
http://www.yasara.org |
| TALOS+ |
(Shen et al., 2009) |
https://spin.niddk.nih.gov/NMRPipe/talos/ |
