KEY RESOURCE TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| GMP-PNP | Sigma | Cat # G0635 |
| TSY | Pacific Biosciences | 100–214-900 |
| Cy3 mono hydrazide | Cytiva | PA13121 |
| Cyanine 3.5 maleimide | AAT Bioquest | Cat # 149 |
| Cy5 mono hydrazide | Cytiva | PA15121 |
| 2’-O-methyltransferase | NEB | Cat # M0336 |
| T4 RNA ligase | ThermoFisher Scientific | Cat # EL0021 |
| T4 RNA ligase 2 | NEB | Cat # M0242S |
| Terminator™ 5ʹ-Phosphate-Dependent Exonuclease | Lucigen | Cat # TER51020 |
| RNA 5’ polyphosphatase | Lucigen | Cat # 136120 |
| RNasin® Ribonuclease Inhibitors | Promega | Cat # N251B |
| DNase I | ThermoFisher Scientific | EN0521 |
| MssI FD | Therno Scientific | Cat # FD1344 |
| Protein kinase R (PKR) | Abcam | Cat # ab32052 |
|
| ||
| Critical commercial assays | ||
|
| ||
| T7 megascript kit | Invitrogen | Cat # AM1334 |
| Vaccinia Capping System | NEB | Cat # M2080S |
| HiScribe RNA synthesis kit | NEB | Cat # E2040S |
| OneStep Human Coupled IVT Kit | ThermoFisher Scientific | Cat # 88881 |
| Luciferase Assay System | Promega | Cat # E1500 |
| Rabbit reticulocyte lysate | Promega | Cat # L4960 |
|
| ||
| Deposited data | ||
|
| ||
| m6A-seq | 22 | SRP121376 |
| GLORI-seq | 9 (Table S1,S5) | GSE210563 |
| eTAM-seq | 23 | GSE201064 |
| A(−3) mRNA cryo-EM map | This paper | EMDB: EMD-17330 |
| m6A(−3) mRNA cryo-EM map | This paper | EMDB: EMD-17329 |
| m6A(−3) mRNA with P-eIF2α cryo-EM map | This paper | EMDB: EMD-18510 |
| mRNA reconstruction atomic model m6 | This paper | PDB: 8P09 |
| m6A(−3) mRNA reconstruction atomic model | This paper | PDB: 8P03 |
|
| ||
| Oligonucleotides | ||
|
| ||
| 5’ UTR sequences | This paper | Table S1 |
| Primers for qRT-PCR | This paper | Table S1 |
|
| ||
| Recombinant DNA | ||
|
| ||
| Plasmid pUC | Addgene | Cat #50005 |
| Plasmid pGL4.51 | Promega | Cat # E1320 |
| Plasmid pUC 5’UTR-less | This study | N/A |
| Plasmid pUC A(−3)-Luc with different 5’UTRs | This study | N/A |
|
| ||
| Software and algorithms | ||
|
| ||
| MATLAB R2021 | Mathworks | N/A |
| RELION | 43 | https://www2.mrc-lmb.cam.ac.uk/groups/scheres/impact.html |
| RELION 3.1 | 56 | https://www2.mrc-lmb.cam.ac.uk/groups/scheres/impact.html |
| MotionCor | 44 | https://emcore.ucsf.edu/ucsf-motioncor2 |
| Chimera, ISOLDE package | 45 | https://www.cgl.ucsf.edu/chimera/ |
| DeepEMancer | 46 | https://tristanic.github.io/isolde/ |
| Bowtie2 | 47 | https://bowtie-bio.sourceforge.net/bowtie2 |
| Cutadapt v1.8.3 | 48 | https://cutadapt.readthedocs.io/en/stable/ |
| STAR | 49 | https://github.com/alexdobin/STAR |
| UMItools | 50 | https://umi-tools.readthedocs.io/en/latest/index.html |
| SAMtools | 51 | http://www.htslib.org |
| HISAT-3N | 52 | http://daehwankimlab.github.io/hisat2/hisat3n/ |
| HOMER | 53 | http://homer.ucsd.edu/homer/index.html |