Hierarchical assembly governs TRIM5α recognition of HIV-1 and retroviral capsids

Figures

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  Fig. 1. Cryotomography and subtomogram averaging of TRIM5α-coated HIV-1 capsid-like tubes. (A) Sections from a tomogram collected at high defocus values (~9 μm), emphasizing the walls of the CA tube (central slice) and the surrounding TRIM5α lattice (peripheral slice). Scale bars, 100 nm. (B to D) Lattice maps showing the final positions and orientations of CA hexamers (B), TRIM dimers (C), and TRIM trimers (D) from a single tube. Each position is displayed on a color scale of red to green, from low to high cross-correlation value as indicated. (E) Combined lattice map with CA hexamers colored in orange, TRIM dimers in cyan, and TRIM trimers in magenta. (F to H) Close-up views.

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  Fig. 2. The structure of TRIM5α bound to HIV-1 capsid-like tubes. (A) Domain organization of TRIM5α. (B to E) Orthogonal views of subtomogram-averaged structures centered on the TRIM5α dimer (B and C) and trimer (D and E). Each map is shown as an isosurface, with a composite PDB model obtained by rigid-body docking of crystal structures (as described in the main text; see also fig. S5). The domains are colored as in (A): B-box 2, orange; coiled coil, green; and SPRY, blue.

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  Fig. 3. The SPRY domain binds to the capsid surface. (A and B) Orthogonal stereoviews of the SPRY dimer reconstruction, with modeled coiled-coil/SPRY dimer. The flexible V1 loops (magenta), which are predicted to directly contact CA are located at the flared regions that join with the capsid surface. A putative SPRY/SPRY dimer interface is indicated by an asterisk. (C) Scatter plot of SPRY dimer positions relative to the closest CA hexamers. Points are colored according to a color gradient that indicates the degree of clustering (red, highest point density and blue, lowest point density). (D) Projection of the CA hexamers in (C), shown for reference.

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  Fig. 4. Structure of TRIM5α in complex with the HIV-1 capsid lattice. (A) Average reconstruction. (B) Views of each of the six edges in the same orientation. (C) Schematic representation of the structure as a hexagon with structurally distinct edges in different colors and labeled from i to vi as shown. Legend indicates the symmetry properties of each edge, which describe the relative arrangements of SPRY and CA. (D) Tiling of a single hexagon is possible only along the iii,vi edge pair trajectory but not the i,iv or ii,v trajectories. (E) Construction of a dihexagon asymmetric unit from the hexagon unit. (F) Tessellation of the dihexagon into a planar lattice.

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  Fig. 5. Paracrystalline architecture of the TRIM5α lattice. (A) Lattice map of a TRIM5α-coated tube. CA hexamers are not shown for simplicity. (B) Same lattice map with geometric shapes traced and colored to aid in visualization. Class 1 hexagons are colored in orange, Class 2 hexagons in green, and grain boundary pentagons and heptagons in blue. (C) Illustration of two planar hexagonal lattice patches (orange and green) connected by pentagons and heptagons.