PMC

eIF4E biological activity and structure. (A) Structure of the m⁷GpppX cap. (B) Crystal structure of eIF4E bound to the m⁷GpppX cap (PDB: 1EJ1). The key tryptophan residues for cap binding are highlighted, in addition to lysines close to the cap-binding pocket.

(A) The active pocket of PCV2 Cap protein (PDB:3R0R), as in red dotted frame. (B) The 2D structure of L11-DYWWQSWE affinity peptide. (C) The key residues and hydrogen bonds (yellow dotted line) of the interaction between the L11 peptide with the PCV2 Cap protein. The graphics were developed by Pymol –0_99rc–bin-win32. (D) The charge interaction between the L11 peptide and the active site of PCV2 Cap protein. The peptide L11 and PCV2 Cap protein are shown in a spherical and ribbon model, respectively. The electrostatic potential ranges from red (most positive ) to purple (most negative).

a, Key steps in translation initiation. The eukaryotic translation initiation factor eIF4E binds directly to the 5′ cap. The heterotrimeric eIF4F complex assembles on the 5′ cap, leading to binding of the 40S ribosomal subunit, assembly of the eukaryotic 80S ribosome and translation initiation. b, Eukaryotic mRNA featuring the cap 0 structure with a recognition site for eIF4E, the site used for chemical modification in this study and the first transcribed nucleotide. c, Structure of eIF4E, highlighting molecular interactions for cap 0 recognition. d, The concept of FlashCaps for light-induced translation. A single photo-cleavable group (red triangle) at the cap 0 impairs binding to eIF4E. FlashCaps are compatible with routine protocols for transcription and transfection. Following light-induced deprotection, the native mRNA with a 5′ cap 0 is released and translated. UTR, untranslated region; PABP, poly(A) binding protein; ORF, open reading frame.

Structure of Cap/Eσ⁷⁰. (A) Schematic illustration of lasso peptide Cap. Residues F18 and N19 were disordered in the crystal structure and are shown as open circles. (B) The atomic model for Cap from the Cap/Eσ⁷⁰ crystal structure is shown along with the 3.25-Å resolution 2F_o − F_c map (blue mesh, contoured at 1.5σ). Carbon atoms of Cap are colored according to A. (C) The overall structure of Cap/Eσ⁷⁰ (DNA is not shown for clarity; SI Appendix, Fig. S1) viewed into the secondary channel. Eσ⁷⁰ is shown as a molecular surface with subunits colored as labeled. Cap is shown as CPK spheres and colored according to A. (D) View of Cap–RNAP interactions. RNAP structural elements that harbor residues interacting with Cap are shown as backbone worms. Residues that interact with Cap are shown in stick format. Cap is shown in stick format with carbon atoms colored according to A. Polar interactions are denoted by dashed gray lines. The RNAP active-site Mg²⁺ is shown as a yellow sphere. (E) Schematic summary of Cap/RNAP contacts. Cap is shown as a backbone worm with side chains of key residues shown. RNAP residues that make only nonpolar contacts are shown as labels with arcs denoting the contacts. The side chains of residues that make polar contacts are shown in stick format (polar contacts are denoted by dashed gray lines).