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. 2023 Nov 30;15(11):mjad076. doi: 10.1093/jmcb/mjad076

Figure 2.

Figure 2

The HIV-1 capsid–natural ligand complexes. The HIV-1 capsid hexamer bound with the cellular factor CypA (PDB: 5FJB; A), IP6 (PDB: 6BHT; B), Sec24C (PDB: 8CL3; C), Nup153 (PDB: 6AYA; D), or CPSF6 (PDB: 7ZUD; E). In each panel, the protein backbone of the six capsid protomers is shown in cartoon representation, with CA-NTDs in light cyan and CA-CTDs in wheat. (A) Upper panel: two molecules of CypA are shown in pink cartoon representation bound to Cyp-loops of non-adjacent capsid protomers within the hexamer. Lower panel: the backbone of CypA is shown in a pink cartoon. Capsid residues in the capsid Cyp-loop that are bound in the active site and CypA residues that make contacts are shown as sticks with hydrogen bonds represented by orange dashed lines. (B–E) IP6 (B), the peptides from Sec24C (C), Nup153 (D), and CPSF6 (E) are shown in stick representation. IP6 is coloured by atom type. Sec24C, Nup153, and CPSF6 are coloured in yellow, green, and magenta, respectively. Lower panels: the capsid residues that interact with bound molecules are labelled and shown in sticks with hydrogen bonds represented by orange dashed lines.