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Fig. 2. | Mobile DNA

Fig. 2.

From: Internal initiation of reverse transcription in a Penelope-like retrotransposon

Fig. 2.

3D structure modeling of the PAc ORF. The dimeric structure was predicted using AlphaFold2 within the Colabfold framework. Three independent replicates, each with 40 cycles, were used. Each replicate consistently yielded the identical dimeric conformation, represented in green and blue (shown in surface and cartoon representations). Two key regions of interaction, outlined by orange dashed circles, stabilize the dimer. The first region features an extended helix (positions 27–173) adopting a head-to-tail homodimeric interaction, predominantly sustained by an intricate hydrophobic network. The second region consists of two helices (positions 232–250 and 795–818) from each dimeric partner, interacting head-to-tail and forming a V shape. This interaction is characterized by two symmetrical salt bridges (indicated by red dashed lines) on the periphery of the interaction patch, encasing a hydrophobic core (highlighted in purple)

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