Fig. 3: RNA–protein contact landscape in the RTIC. | Nature Communications

Fig. 3: RNA–protein contact landscape in the RTIC.

From: High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs

Fig. 3

a RT–dsRNA contact landscape of the miniRTIC. Secondary structure of the extended PBS helix (vRNA template = gold, tRNA primer = red), and associated contacts with protein residues. b RT–dsDNA contact landscape of an elongation complex (Huang et al.20) reveals more contacts compared to the RTIC. Primer strand on bottom, template strand on top. Hydrogen bonds specified in solid red. Solid black line indicates cross-link. RNase H primer grip abbreviated as “RNase H (PG)”. c Top-down view of miniRTIC p66 subunit and the extended PBS helix. Thumb and RNase H domain residues of the p66 subunit (purple) contact the minor groove of the PBS helix (vRNA template = gold, tRNA primer = red). d View of p66 thumb contacts with the tRNA primer backbone. Residues N255 and K259 on αH helix interact with the backbone of nucleotides (nts) C72 and G73. e View of p66 thumb contacts with the vRNA template backbone. Residues N265 on αH helix and residues L283 and R284 on αI helix contact the backbone of nts C187, C188, and C189. f View of RNase H domain primer grip contacts with the tRNA backbone. Residues Y501, Q475, and T473 interact with nts U60 and C61. g View of residues adjacent to RNase H-active site contacting the vRNA template. Residues N474, R557, R448, and H539 interact with nts C199, U200, and U201. Nucleotides U200 and U201 are a part of the extended PBS helix.

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