KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-NBD antibody | Acris Antibodies GmbH | Cat#BP086; RRID: AB_972399 |
| Mouse monoclonal Anti-pan-eIF4A antibody | Santa Cruz Biotechnology | Cat#sc-377315; RRID: AB_2868449 |
| Rabbit polyclonal anti-eIF4A1 antibody | Cell Signaling Technology | Cat#2490S; RRID: AB_823487 |
| Rabbit polyclonal anti-eIF4A2 antibody | Abcam | Cat#ab31218; RRID: AB_732123 |
| Mouse monoclonal anti-β-actin antibody | LI-COR Biosciences | Cat#926-42212; RRID: AB_2756372 |
| Rabbit monoclonal anti-DDX3X antibody | Cell Signaling Technology | Cat#8192S; RRID: AB_10860416 |
| Goat polyclonal anti-rabbit IgG antibody conjugated with IRDye 800CW | LI-COR Biosciences | Cat#926-32211; RRID: AB_621843 |
| Goat polyclonal anti-mouse IgG antibody conjugated with IRDye800CW | LI-COR Biosciences | Cat#926-32210; RRID: AB_621842 |
| Bacterial and Virus Strains | ||
| E. coli: BL21 Star (DE3) | Thermo Fisher Scientific | Cat#C601003 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Rocaglamide A | Sigma-Aldrich | Cat#SML0656 |
| Aglafoline | MedChem Express | Cat#HY-19354 |
| RocA-O-NBD | This study | N/A |
| Adenylyl-imidodiphosphate (AMP-PNP) | Roche | Cat#10102547001 |
| ADP | Wako Pure Chemical Industries | Cat# 019-25091 |
| D-biotin | Invitrogen | Cat#B20656 |
| Trifluoroacetic acid (TFA) | Kanto Chemical Co., Inc. | Cat#40578-1B |
| Distilled water containing 0.1% (v/v) formic acid (FA) | Kanto Chemical Co., Inc. | Cat#01922-64 |
| Acetonitrile (MeCN) containing 0.1% (v/v) FA | Kanto Chemical Co., Inc. | Cat#16245-64 |
| Recombinant protein: His-DDX3X helicase core WT | This study | N/A |
| Recombinant protein: HIs-DDX3X helicase core Pro324Thr | This study | N/A |
| Recombinant protein: His-DDX3X helicase core Val328Leu | This study | N/A |
| Recombinant protein: His-DDX3X helicase core Gln360Pro | This study | N/A |
| Recombinant protein: His-DDX3X helicase core Gln360Leu | This study | N/A |
| Recombinant protein: His-DDX3X helicase core Arg363Asn | This study | N/A |
| Recombinant protein: His-eIF4A1 WT | Iwasaki et al. 2019 | N/A |
| Recombinant protein: His-eIF4A1 Phe163Leu-Ile199Met | Iwasaki et al. 2019 | N/A |
| Recombinant protein: His-eIF4A2 WT | This study | N/A |
| Recombinant protein: His-SBP-eIF4A1 | This study | N/A |
| Recombinant protein: His-SBP-DDX3X helicase core | This study | N/A |
| Sequencing Grade Modified trypsin | Promega | Cat#v5113 |
| Lysyl endopeptidase (Mass Spectrometry Grade) | FUJIFILM Wako Chemical | Cat#125-05061 |
| RNase I | Epicentre | Cat#N6901K |
| Critical Commercial Assays | ||
| DMEM (1×) + GlutaMAX-I | Thermo Fisher Scientific | Cat#10566-016 |
| High Glucose DMEM | Nacalai Tesque | Cat#16971-55 |
| RPMI 1640 Medium | Thermo Fisher Scientific | Cat#A1049101 |
| Ni-NTA Agarose | Qiagen | Cat#30210 |
| HiTrap Heparin HP column 1 ml | GE Healthcare | Cat#17040601 |
| NAP-5 | GE Healthcare | Cat#17085302 |
| PD-10 | GE Healthcare | Cat#17085101 |
| Vivaspin 6, 10 kDa MWCO | GE Healthcare | Cat#28932296 |
| Amicon Ultra-4, 10 kDa MWCO | Millipore | Cat#UFC8010 |
| T7-Scribe Standard RNA IVT Kit | CELLSCRIPT | Cat#C-AS3107 |
| ScriptCap m7G Capping System | CELLSCRIPT | Cat#C-SCCE0625 |
| ScriptCap 2′-O-Methyltransferase Kit | CELLSCRIPT | Cat#C-SCMT0625 |
| A-Plus Poly(A) Polymerase Tailing Kit | CELLSCRIPT | Cat#C-PAP5104H |
| Rabbit Reticulocyte Lysate System, Nuclease Treated | Promega | Cat#L4960 |
| Renilla-Glo Luciferase Assay System | Promega | Cat#E2720 |
| MicroSpin G-25 Column | GE Healthcare | Cat#27532501 |
| Dynabeads Protein G | Thermo Fisher Scientific | Cat#10004D |
| Protein G Mag Sepharose beads | GE Healthcare | Cat# 28-9440-08 |
| MonoSpin C18 S | GL Science | Cat#5010-21701 |
| TransIT-X2 Transfection Reagent System | Mirus | Cat#MIR6000 |
| RealTime-Glo MT Cell Viability Assay System | Promega | Cat#G9713 |
| Monolith His-Tag Labeling Kit RED-tris-NTA | NanoTemper | Cat#MO-L018 |
| Dynabeads M-270 Streptavidin | Thermo Fisher Scientific | Cat#DB65305 |
| Oligo Clean & Concentrator Kit | Zymo Research | Cat#D4061 |
| Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) | Illumina | Cat#MRZG12324 |
| Deposited Data | ||
| Ribosome profiling of cancer cell lines with RocA treatment, raw and processed data | This study | GEO: GSE148636 |
| RNA-Bind-n-Seq of eIF4A1 and DDX3X with RocA treatments, raw and processed data | This study | GEO: GSE150111 |
| Aglaia RNA-Seq, raw data | Iwasaki et al. 2019 | SRA: SRR5947159 |
| Human eIF4A1•AMPPNP•RocA•(AG)5 complex structure | Iwasaki et al. 2019 | PDB: 5ZC9 |
| Human DDX3X core•AMPPNP structure | Floor et al. 2016 | PDB: 5E7M |
| Original images used for the figures | This study | Mendeley Data: doi: 10.17632/syfc38x8md.1 |
| Experimental Models: Cell Lines | ||
| T-Rex-293 (HEK) | Thermo Fisher Scientific | Cat#R71007 |
| T-REx293 SBP-eIF4A1 (Phe163Leu-Ile199Met) eIF4A1SINI | Iwasaki et al. 2019 | N/A |
| Hs 936.T | American Type Culture Collection (ATCC) | Cat#CRL-7687 |
| A375 | American Type Culture Collection (ATCC) | Cat#CRL-1619 |
| NCI-H1650 | American Type Culture Collection (ATCC) | Cat#CRL-5883 |
| NCI-H520 | American Type Culture Collection (ATCC) | Cat#HTB-182 |
| Oligonucleotides | ||
| FAM labeled RNA (AG)10: FAM-AGAGAGAGAG AGAGAGAGAG | Hokkaido System Science, Iwasaki et al. 2019 | N/A |
| FAM labeled RNA (UC)10:FAM-UCUCUCUCUCUCUCUCUCUC | Hokkaido System Science, This paper | N/A |
| (AG)5A: AGAGAGAGAGA | Fasmac, This paper | N/A |
| DDX3X-specific siRNA | Dharmacon | Cat# L-006874-02-0005 |
| eIF4A2-specific siRNA | Dharmacon | Cat# L-013758-01-0005 |
| control siRNA | Dharmacon | Cat# D-001206-13-05 |
| CTCTTTCCCTACACGACGCTCTTCCGATCT-N30-ATCGTAGATCGGAAGAGCACACGTCTGAA (letters in bold represent the DNA sequence and N represents random the RNA sequence) | Gene Design | N/A |
| Recombinant DNA | ||
| pColdI-DDX3X helicase core WT | This study | N/A |
| pColdI-DDX3X helicase core Pro324Thr | This study | N/A |
| pColdI-DDX3X helicase core Val328Leu | This study | N/A |
| pColdI-DDX3X helicase core Gln360Pro | This study | N/A |
| pColdI-DDX3X helicase core Gln360Leu | This study | N/A |
| pColdI-DDX3X helicase core Arg363Asn | This study | N/A |
| pColdI-eIF4A1 WT | Iwasaki et al. 2019 | N/A |
| pColdI-eIF4A1 Phe163Leu-Ile199Met | Iwasaki et al. 2019 | N/A |
| pColdI-eIF4A2 WT | This study | N/A |
| pColdI-SBP-eIF4A1 | This study | N/A |
| pColdI-SBP-DDX3X helicase core | This study | N/A |
| psiCHECK2-CAA repeats | Iwasaki et al. 2016 | N/A |
| psiCHECK2-7×AGAGAG motifs | Iwasaki et al. 2016 | N/A |
| Software and Algorithms | ||
| Igor Pro Version: 8.01 | WaveMetrics | https://www.wavemetrics.com/products/igorpro |
| MASCOT server version: 2.6 | Matrix Science | https://www.matrixscience.com/ |
| Proteome Discoverer version: 1.3 | Thermo Fisher Scientific | N/A |
| Xcalibur software version: 2.1 or 4.1 | Thermo Fisher Scientific | N/A |
| Other | ||
| NGC chromatography system | Bio-Rad | N/A |
| GloMax Navigator | Promega | Cat#GM2010 |
| Image Pharos FX | Bio-Rad | N/A |
| ODYSSEY CLx | LI-COR Biosciences | N/A |
| LTQ Orbitrap XL mass spectrometer | Thermo Fisher Scientific | N/A |
| nanoESI source | Nikkyo Technos | N/A |
| UltiMate 3000 nano LC system | Thermo Fisher Scientific | N/A |
| Infinite F-200 PRO | TECAN | N/A |
| Monolith NT.115 | NanoTemper | N/A |