Fig. 2: Cryo-EM structure of reactant state R-1 of the RT-T/P-dATP complex.
From: Structural basis of deoxynucleotide addition by HIV-1 RT during reverse transcription
a Overlay of the structures of the RT-T/P complex (red) and state R-1 of the RT-T/P-dATP complex (yellow) highlighting conformational changes in the RT active site that occur upon dATP binding (black arrows). The protein backbone displayed in the cartoon and key residues displayed as ball-and-stick. Map for state R-1 is displayed in yellow mesh, with sharpening at B-factor −60 Å2 and contoured at 10σ. The map for the RT-T/P complex is displayed in red mesh, unsharpened, and contoured at 7σ. b Site B Mg2+ coordination in state R-1 structure, yellow mesh contoured at 10σ. Distances (in Å) are indicated next to dashed lines. c Watson–Crick pairing of dATP with the templating (i-1) base, induces repositioning of the template strand (black arrows). d Large-scale conformational changes of the P66 fingers subdomain (residues 1–85 and 118–155) are observed (black arrows) upon dATP binding. e Surface representation (shown in red) of the Open active site in the dNTP-free RT-T/P complex and f the Closed active site of RT-T/P-dATP complex (shown in yellow) as a result of dATP binding (shown in ball-and-stick). Reposition of key residues D110 and K220 induces a tighter pocket in state R-1 evidenced by the extra bump region absent in RT-T/P (see e dashed line).
