Extended Data Fig. 8: Comparison of ORF2p with other RTs.
From: Structures, functions and adaptations of the human LINE-1 ORF2 protein

a, Domain organization and sequence alignment of LINE-1 ORF2 (L1RP locus, GenBank AF148856) with other reverse transcriptase (RT) containing proteins: Bombyx mori R2Bm RT (PDB 8gh6, GenBank AAB59214), group IIC intron (PDB 6ar1, Uniprot E2GM63), non-LTR element HERV-K (PDB 7sr6, clone 10.9, GenBank AF080231), and retrovirus HIV-1 RT (PDB 4pqu, UniProt: P03366.3). Sequences were aligned structurally using ChimeraX software and via the conserved RT sequence blocks (0–7)75,76, with degree of sequence conservation and common structural features noted below. b, Comparison of the N-terminal extension and 5’ template contacts between (from left to right) LINE-1 ORF2p, HERV-K RT (PDB 7sr6), group IIC intron (PDB 6ar1) and R2Bm (PDB 8gh6). The ORF2p PIP box helix occupies the space of the HIV αA helix and a tower-like helix in R2Bm that is not a PIP box. The template makes extensive contacts with ORF2p and takes a distinct 5’ path upstream of the active site than in the other RTs, guided by adaptations in fingers (L535), palm (I642), and tower (Q338). c, Comparison of downstream primer-binding surfaces across the four RTs; primer contacts with thumb helix clamps (lime green) shown inset. The thumb in ORF2, R2Bm, and GSI-IIC is permuted relative to HERV-K (and HIV), with the primer-contacting helix clamp on helix #2, whereas it is on helix #1 in HERV-K. ORF2p wrist also contacts the template, the R2 linker makes a smaller set of contacts, and these bases are exposed in HERV-K and GSI-IIC. d, Models of ORF2p Core, HERV-K RT, and GSI-IIC RT77 aligned by palm superposition. The RT domains of GSI-IIC and ORF2p Core are more similar to each other than to HERV-K. The HERV-K linker and RNase H domains occupy a similar position to the ORF2p wrist, and GSI-IIC D ___domain is in a similar position to ORF2p CTD and R2 CCHC (see Supplementary Fig. 11).