Fig. 1: Pathogenic replication cycle of L1 and the 2.1 Å resolution crystal structure of human ORF2p core in a ternary complex.

a, The 6 kb human L1 element contains an internal 5′ untranslated region (UTR) promoter, two proteins ORF1p and ORF2p in a bicistronic arrangement separated by 63 nt and a short 3′ UTR. b, Replication cycle of L1, a streamlined self-copying DNA parasite. Derepression of genomic L1s results in Pol II transcription and export of the L1 RNA, which is translated to form an RNP complex containing one copy ORF2p, a multifunctional enzyme, and many copies of ORF1p, a homotrimeric chaperone involved in nuclear entry that can form phase-separated granules. Canonically, in the nucleus, ORF2p integrates a new copy of the L1 RNA into the genome in a mechanism termed TPRT, in which cleavage by the L1 EN liberates a genomic DNA (gDNA) 3′-OH used to prime reverse transcription of the L1 RNA, followed by insertion by poorly understood mechanisms (‘Discussion’, Fig. 6). Non-canonical outcomes contribute to pathology: failed insertions and aberrant EN activity result in DNA damage and translocations, and aberrant cytosolic RT activity generates inflammatory RNA:DNA hybrids. Host proteins (not shown) are associated at every step and may repress L1 or function as essential cofactors. c, Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis of pure, monodisperse 97 kDa ORF2p core after size exclusion chromatography. d, Two new domains (tower and wrist) and three canonical RT subdomains (fingers, palm, thumb) coordinate with a hybrid duplex RNA template (purple) and DNA primer (cyan) and incoming dTTP nucleotide (yellow) for ORF2p core RT activity in the 2.1 Å resolution crystal structure in a ‘right-hand’ RT fold that is uniquely adapted. All five ORF2p core domains contact the template or primer, and numerous residues contact the incoming base; protein contacts are summarized in the inset schematic.