Retroviruses enclose the viral RNA genome, select enzymes, and accessory proteins in spheroidal capsids, the assembly and stability of which are critical to progression through the viral life cycle. The HIV-1 capsid is an asymmetric, conical-shaped shell made up of hexameric and pentameric units of the capsid protein (CA) in a hexagonal lattice. Structures of the basic CA assembly units have been determined by X-ray crystallography, however, detailed atomic structural information on the assembled capsid and on contacts between the assembly units has been limited. Here, we report the structure of a tubular HIV-1 CA assembly at 9 Å resolution as determined by cryo-EM. The structure reveals novel hydrophobic interactions that are surrounded by charged polar residues at the three-fold interface.
Mutagenesis experiments confirmed that hydrophobic residues at the center of a three-helix bundle are critical for capsid assembly, stability, and viral infectivity. Furthermore, the cryo-EM structure allowed unambiguous modeling and refinement by large-scale molecular dynamic simulation, resulting in all-atom models for the essential hexamer-hexamer and pentamer-hexamer interactions and the entire CA assembly comprising 13 million atoms. Incorporation of pentamers into the hexagonal lattice induces acute surface curvature while maintaining all the essential inter-subunit interactions, thereby revealing quasi-equivalence in the HIV-1 capsid lattice. We anticipate that our new CA assembly structure and all-atom models provide a valuable platform for further studies of capsid function and for targeted pharmacological intervention.