KEY RESOURCES TABLE
REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Bacterial and Virus Strains | ||
NEB DH5α competent E.coli | NEB | cat#C2987 |
BL21(DE3) competent E.coli | NEB | cat#C2527 |
Chemicals, Peptides, and Recombinant Proteins | ||
m7GpppG | NEB | cat#S1405S |
Sypro Orange q | Thermo Fischer Scientific | cat#S6650 |
T4 PNK | NEB | cat#M0201 |
vaccinia capping enzyme | NEB | cat#M2080 |
α-32P-GTP | Perkin Elmer | cat#BLU506H250UC |
His-Pur NiNTA | Thermo Fischer Scientific | cat#88222 |
HiTrap Q | GE | cat#17115401 |
HiTrap SP | GE | cat#17115201 |
HiTrap Butyl | GE | cat#28411005 |
10K MWCO | Millipore | cat#C7715 |
calf intestinal phosphatase | Roche | cat#11097075001 |
Deposited Data | ||
Apo X-ray crystal structure of DM15 | (Lahr et al., 2015) | PDBID: 4ZC4 |
F844YR847E DM15 X-ray crystal structure | This study | PDBID: 6PW3 |
Oligonucleotides | ||
Forward and reverse primers for K924D Mutation of LARP1 DM15 5’CTGGGCCTTCTTGAAA TATTCCGACGCCAAAAAT TTGGAC3’ 5’GTCCAAATTTTTGGCGTC GGAATATTTCAAGAAGGC CCAG3’ |
Sigma | N/A |
Forward and reverse primers for K924A Mutation of LARP1 DM15 5’CTGGGCCTTCTTGAAATATTCCGCAGCCAAAAAT TTGGAC3’ 5’GTCCAAATTTTTGGCTGC GGAATATTTCAAGAAGGC CCAG3’ |
Sigma | N/A |
Forward and reverse primers for K921A Mutation of LARP1 DM15 5’caaatttttggctttggaatatgccaagaaggcccagaacttctcc 3’ 5’ggagaagttctgggccttcttggcatattccaaagccaaaaatttg3’ |
Sigma | N/A |
Forward and reverse primers for K815A Mutation of LARP1 DM15 5’ cacaacacgtctaccatgcgtatcgtaggcgctgcc 3’ 5’ ggcagcgcctacgatacgcatggtagacgtgttgtg 3’ |
Sigma | N/A |
Forward and reverse primers for F844YR847E Mutation of LARP1 DM15 R847E 5’ catctttttgttgaagtgatcctcgaggaagaaggaccagaagcg 3’ 5’ cgcttctggtccttcttcctcgaggatcacttcaacaaaaagatg 3’ F844YR847E 5’catacatctttttgttgaagtgatcctcgaggaaataggaccagaagcggaagagtgtgt 3’ 5’acacactcttccgcttctggtcctatttcctcgaggatcacttcaacaaaaagatgtatg 3’ |
Sigma | N/A |
Splint adapter 5’ CTTGAAGCAGCTGAACGCCTCCGAGGCGCCACGGAAAAGAGG 3’ | Sigma | N/A |
Recombinant DNA | ||
human LARP1 isoform 2 | ThermoFisher | BC033856 |
Software and Algorithms | ||
PDB2PQR 2.1.1 | (Dolinsky et al., 2007; Dolinsky et al., 2004) | http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/ |
Ambertools18 | (Case et al., 2017) | http://ambermd.org/AmberTools.php |
NAMD 2.9 | (Kale et al., 1999; Phillips et al., 2005) | http://www.ks.uiuc.edu/Research/namd/ |
MDAnalysis 0.16.2 | (Michaud-Agrawal et al., 2011) | https://www.mdanalysis.org/ |
FTMap | (Kozakov et al., 2015; Ngan et al., 2012) | https://ftmap.bu.edu/ |
VMD | (Humphrey et al., 1996) | https://www.ks.uiuc.edu/Research/vmd/ |
Phenix 1.13–2998 | (Adams et al., 2010) | https://www.phenix-online.org/ |
POVME 2.0 | (Durrant et al., 2014) | rocce-vm0.ucsd.edu/data/sw/hosted/POVME/ |
QuantStudio™ Design & Analysis Software V 8.1.0.0 | ThermoFisher Scientific | https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/ab-quantstudio-3-and-5-real-time-pcr-system.html |
PyMOL Molecular Graphics System, Version 1.8.6.0. | (DeLano, 2002) | https://pymol.org/2/ |
GraphPad Prism 7.0 | GraphPad Software | Prism - graphpad.com |
SPSS Statistics V.25 | IBM | https://www.ibm.com/products/spss-statistics |