KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and Virus Strains | ||
| E.coli BL21 Star (DE3) | Invitrogen | C601003 |
| E.coli DH5α | Invitrogen | 18265017 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| T7 RNA polymerase | Thermo Scientific | EP0111 |
| Avian Myeloblastosis Virus Reverse Transcriptase |
Promega | M5108 |
| T4 Polynucleotide Kinase | New England Biolabs | M0201S |
| tRNA calf liver | Promega | Y209X |
| Rabbit reticulocyte lysate | Green Hectares | n/a |
| Flexi Rabbit Reticulocyte Lysate System | Promega | L4540 |
| TNT® T7 Insect Cell Extract Protein Expression System | Promega | L1101 |
| Isopropyl-beta-D-thiogalactoside | Gold Biotechnology | I2481C100 |
| Ni-NTA Agarose | QIAGEN | 30230 |
| MonoS 5/50 GL column | Cytiva Life Sciences | 17516801 |
| MonoQ 5/50 GL column | Cytiva Life Sciences | 17516601 |
| Superdex 200 Increase 5/150 GL | Cytiva Life Sciences | 28990945 |
| RiboLock RNase inhibitor | Thermo Scientific | EO0381 |
| [35S]-methionine | Perkin Elmer | NEG009T |
| [γ−32P]ATP | Perkin Elmer | BLU002Z |
| [α−32P]-UTP | Perkin Elmer | BLU007H |
| BamHI | New England Biolabs | R0136S |
| BstN1 | New England Biolabs | R0607S |
| EcoRV | New England Biolabs | R0195S |
| EcoRI | New England Biolabs | R0101S |
| HindIII | New England Biolabs | R0104S |
| XbaI | New England Biolabs | R0145S |
| Deposited Data | ||
| Raw data | Mendeley Data | https://data.mendeley.com/datasets/wx2ypvtxh8/draft?a=8017d354-6b04-4735-a5f8-464205fbbad9 |
| Structure of [80S-HalV IGR IRES] complex(rotated conformation) | This paper | PDB: 7A01 |
| Structure of [80S-HalV IGR IRES] complex (unrotated conformation) | This paper | PDB: 6ZVK |
| Cryo-electron microscopy map of [80S-HalV IGR IRES] complex (rotated conformation) | This paper | EMDB: EMD-11590 |
| Cryo-electron microscopy map of [80S-HalV IGR IRES] complex (unrotated conformation) | This paper | EMDB: EMD-11459 |
| Oligonucleotides | ||
| ssDNA (GATTGCTTGTTTAG) HalV | Thermo Fisher | N/A |
| ssDNA (GTAATTCCTTCGCTAAC) CrPV | Thermo Fisher | N/A |
| Recombinant DNA | ||
| pQE31-His6-eIF1 | Pisarev et al., 2007 | N/A |
| pET28-His6-eIF1A | Pisarev et al., 2007 | N/A |
| pET15b-His6-eIF4A | Pisarev et al., 2007 | N/A |
| pET15b-His6-eIF4B | Pisarev et al., 2007 | N/A |
| pET28-eIF4G736–1115 | Pisarev et al., 2007 | N/A |
| pET23b-eRF1-His6 | Pisarev et al., 2007 | N/A |
| pET23b-His6-eRF3a(139–499) | This work | N/A |
| pET-15b PAI-RBP | Heaton et al., 2001 | N/A |
| pMetRS | Lomakin et al., 2006 | N/A |
| pUC57-tRNASer (UCU) | Zinoviev et al., 2015 | N/A |
| pUC57-T7-Stem-HalV nt.6211–7460 | This work | N/A |
| pUC57-T7-Stem-HalV nt.6205–6513 | This work | N/A |
| pUC57-T7-Stem-HalV nt.6268–6513 | This work | N/A |
| pUC57-T7-Stem-HalV nt.6280–6513 | This work | N/A |
| pUC57-T7-Stem-HalV nt.6284–6513 | This work | N/A |
| pUC57-T7-Stem-HalV nt.6297–6513 | This work | N/A |
| pUC57-T7-Stem-HalV nt.6327–6513 | This work | N/A |
| pUC57-T7-Stem-HalV nt.6268–6483 | This work | N/A |
| pUC57-T7-Stem-HalV IGR-GUS | This work | N/A |
| pUC57-T7-HalV(2nt. L2 loop) | This work | N/A |
| pUC57-T7-HalV(6nt. L2 loop) | This work | N/A |
| pUC57-T7-HalV(+4nt. L2 loop) | This work | N/A |
| MC Stem-HalV | Abaeva et al., 2016 | N/A |
| pUC57-CrPV nt. 5997–6320 | This work | N/A |
| pUC57-CrPV5997–6320-Stop | This work | N/A |
| HalV PKII+CrPV PKI/SerStop | This work | N/A |
| pUC57-T7-CrPV PKII/PKIII+HalV PKI(SerStop) | This work | N/A |
| pUC57-T7-HalV PKI/II + CrPV PKIII | This work | N/A |
| pUC57-T7-CrPV ΔPKIII + HalV L2 loop | This work | N/A |
| pUC57-T7-CrPV ΔPKIII+HalV extended L2* loop | This work | N/A |
| Software and Algorithms | ||
| BLASTN | https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | RRID:SCR_001598 |
| BLASTX | https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&BLAST_SPEC=&LINK_LOC=blasttab&LAST_PAGE=blastn | RRID:SCR_001653 |
| EMBOSS Matcher | https://www.ebi.ac.uk/Tools/psa/emboss_matcher/ | RRID:SCR_017252 |
| Clustal Omega | https://www.ebi.ac.uk/Tools/msa/clustalo/ | RRID:SCR_001591 |
| CentroidFold | https://www.ncrna.org/centroidfold | RRID:SCR_017253 |
| Mfold | http://www.unafold.org/ | RRID:SCR_008543 |
| pKISS | https://bibiserv.cebitec.uni-bielefeld.de/pkiss | RRID:SCR_017256 |
| ImageQuant TL version 8.1 | Cytiva | RRID:SCR_014246 |
| Ugene v. 1.22 | http://ugene.net/ | RRID:SCR_005579 |
| MotionCor | https://emcore.ucsf.edu/ucsf-software | N/A |
| Gctf | https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/ | RRID:SCR_016500 |
| RELION 3.0 | https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page | RRID:SCR_016274 |
| ResMap | http://resmap.sourceforge.net/ | N/A |
| UCSF Chimera | https://www.cgl.ucsf.edu/chimera/ | RRID:SCR_004097 |
| UCSF Chimera X | https://www.cgl.ucsf.edu/chimerax/ | RRID:SCR_015872 |
| Pymol v. 1.8.0.5, v. 2.0.6 | https://pymol.org/2/ | RRID:SCR_000305 |
| Assemble v. 2 | http://bioinformatics.org/S2S/ | https://pubmed.ncbi.nlm.nih.gov/20562414/ |
| Molecular Dynamic Flexible Fitting | https://www.ks.uiuc.edu/Research/mdff/ | https://www.sciencedirect.com/science/article/pii/S0969212608001330 |
| Visual Molecular Dynamics | https://www.ks.uiuc.edu/Research/vmd/ | https://nlm.nih.gov/8744570/ |
| NAMD v. 2 | http://www.ks.uiuc.edu/Research/namd/ | RRID:SCR_014894 |
| Phenix v. 1.10.1–2155, v. dev-2474 | http://www.phenix-online.org/ | RRID:SCR_014224 |
| Phenix v. dev.3885 | http://www.phenix-online.org/ | https://journals.iucr.org/d/issues/2018/09/00/kw5139/index.html |
| Coot v. 0.8.2 and v. 0.9-pre EL | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ | RRID:SCR_014222 https://pubmed.ncbi.nlm.nih.gov/29872001/ |
| EPU software | FEI Company | n/a |
| Molprobity | http://molprobity.biochem.duke.edu | RRID:SCR_014226 |
| Phylogeny.fr | http://phylogeny.lirmm.fr/phylo_cgi/index.cgi | RRID:SCR_010266 |
| IQ-TREE | http://www.iqtree.org/ | RRID:SCR_017254 |