Extended Data Fig. 5: LSU interactions with tRNA and the SSU in each characterized ribosome structure along the translocation reaction coordinate.
From: Structural basis of early translocation events on the ribosome
a, Location of intersubunit bridge B1 on the ribosome (top, left) and overlay of uL31 model (dark blue) depicting the conformational change during translocation (top, right). Sphere is positioned on residue Ile66 (Cα). Bottom, bridge B1 interactions between the LSU central protuberance and the SSU head domain (purple) in each structural state, including the ASF (H38, dark green) to uS13 (B1a), uL5 to uS13 (B1b) and uL31 to uS13/uS19 (B1c). Threshold σ = 4. b, Location of the L1 stalk, uL5 (dark grey), uL16 (light grey) and ASF (dark green) on the INT1 ribosome (top). L1 stalk positioning and interaction with deacyl-tRNA (yellow/orange) elbow in each classified structure (bottom). c, Bridge B1 interactions between the central protuberance and deacyl-/peptidyl-tRNA from PRE-C (top) to POST (bottom). P-site tRNA G19–C56 pair contacts include LSU H84 base A2309 and uL5 N-terminal Arg80. A-site tRNA contacts include G19–C56 pair coordination by ASF base A896 and TΨC stem packing against uL16 residues Arg6 and Lys7. A site (green circle), P site (yellow circle), E site (orange circle) regions are shown. d, Locally filtered electron density illustrating peptidyl transferase centre interactions along the translocation interaction coordinate. Watson–Crick pairing between the 3′-CCA tRNA ends and the peptidyl transferase centre. P loop (LSU rRNA 2251–2253, 2450–2451), dark blue; A loop (LSU rRNA 2553–2555, 2582–3585, dark grey; peptide, red; LSU base A2602, dark green; deacyl-tRNA, yellow-orange; peptidyl-tRNA, green; Threshold σ = 7. Camera perspective is identical for images within each panel. Alignment on the LSU core. See also Supplementary Video 2.
