1. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability
by Anna T. Gres, Karen A. Kirby, Vineet N. KewalRamani, John J. Tanner, Owen Pornillos, and Stefan G. Sarafianos
Science
Volume 349(6243):99-103
July 3, 2015
Published by AAAS

2. Fig. 1 Crystal structure of native CA
Fig. 1 Crystal structure of native CA. (A) Secondary structure and ribbon diagram of native CA. The CANTD comprises β hairpin (residues 1 to 13, brown), CypA-BL (85 to 93, light blue), and seven α helices: H1 (17 to 30, yellow); H2 (36 to 43, black); H3 (49 to 57, purple); and H4 (63 to 83), H5 (101 to 104), H6 (111 to 119), and H7 (126 to 145) in gray.
Crystal structure of native CA. (A) Secondary structure and ribbon diagram of native CA. The CANTD comprises β hairpin (residues 1 to 13, brown), CypA-BL (85 to 93, light blue), and seven α helices: H1 (17 to 30, yellow); H2 (36 to 43, black); H3 (49 to 57, purple); and H4 (63 to 83), H5 (101 to 104), H6 (111 to 119), and H7 (126 to 145) in gray. The CACTD comprises the 310 helix (residues , green) and four α helices: H8 (161 to 173, gray), H9 (179 to 192, orange), H10 (196 to 205, blue), and H11 (211 to 217; pink). (B) Application of sixfold crystallographic symmetry generates the native CA hexagonal lattice. A single native CA molecule is shown in surface view representation (pink, CANTD; red, CACTD). (C) The six native CA subunits in a hexamer are related by sixfold crystallographic symmetry (yellow hexagon); CA subunits from neighboring hexamers are related by twofold (orange ovals) and threefold (pink triangles) crystallographic symmetry, shown at the interhexamer interfaces. (D) Orthogonal views of three native CA hexamers colored as in (A). The hexamers are stabilized by interactions at the sixfold (brown, β hairpin; yellow, H1; black, H2; purple, H3), twofold (green, 310; orange, H9), and threefold (blue, H10; pink, H11) interfaces. (E) Interhexamer interactions at the twofold interface. Interpretable electron density is now observed for all residues at the twofold interface of native CA (2.4 Å; 2Fobs – Fcalc; σ = 1.2), including residues 176 to 187, which were previously disordered in cross-linked hexamer structures.
Anna T. Gres et al. Science 2015;349:99-103
Published by AAAS

3. Fig. 2 Interhexamer interactions at the twofold and threefold interfaces.
Interhexamer interactions at the twofold and threefold interfaces. Stereo views of CACTD regions that are related by twofold [(A) and (C)] or threefold [(B) and (D)] symmetry from native CA [(A) and (B)] and dCA [(C) and (D)]. The twofold interface comprises helices H9 and 310 in (A) and (C). The threefold interface comprises helices H10 and H11 in (B) and (D). Ordered water molecules (spheres) at the twofold (A) and threefold (B) interfaces of native CA are modeled in 2.4 Å simulated annealing omit Fobs – Fcalc electron density maps at σ = 2.5 (green mesh). B-factors of refined waters were between 30 to 50 Å2 and matched well with those of interacting atoms from S149, E175, Q176, W184, I201, and A204. Helices are shown in cartoon representation; black dashed lines between residues (in sticks) indicate that they are within ~4 Å of each other. No water molecules are present at the twofold and threefold interfaces of dCA [(C) and (D)].
Anna T. Gres et al. Science 2015;349:99-103
Published by AAAS

4. Fig. 3 Changes at the intrahexamer interfaces.
Changes at the intrahexamer interfaces. (A) Stereo view of intrahexamer CANTD-CANTD and CANTD-CACTD intersubunit interfaces. Two neighboring CA subunits are shown as cartoons outlined for clarity (CANTDs in lighter colors than the corresponding CACTDs). Sites of varying interactions among native CA, dCA, CAXL, and CAPF74 are marked in blue and orange for CANTD-CANTD interfaces or brown and pink for CANTD-CACTD interfaces. (B) Intrasubunit rearrangement linked to changes at the twofold interface. Enlarged stereo view of the boxed region shows changes in the position of H9 helices in neighboring subunits (marked with prime symbols). Least-squares superposition (residues 143 to 174 and 192 to 219) of dCA (cyan, CANTD; darker blue, CACTD) on native CA (pink, CANTD; red, CACTD) is shown. Crystal dehydration results in a slight extension of helix H8 (small blue arrow), interaction of R143 with the main-chain E175 carbonyl instead of Q176, and repositioning of the helix H9 (black arrow). In dCA, W184′ from the H9′ helix (light blue for dCA and light pink for CA) forms a hydrogen bond with main-chain E175 carbonyl from a neighboring subunit, whereas in native CA, W184′ interacts with Q176 and the side chain of E175 through water-mediated contacts. Moreover, in dCA, R143 also interacts with E187′ and T188′ from the neighboring subunit, thus becoming a part of the twofold interface. Black dashed lines connect residues or waters that interact through hydrogen bonds.
Anna T. Gres et al. Science 2015;349:99-103
Published by AAAS

5. Fig. 4 Effects of PF74 on HIV-1 CA structure.
Effects of PF74 on HIV-1 CA structure. (A) PF74 binding at the CANTD-CACTD interfaces of neighboring subunits within a CA hexamer. Top view of CAPF74 hexamers is shown (side view is shown in fig. S6A). There is one PF74 molecule bound to every CA subunit at sites that are distant to the threefold interface (black triangle). CANTDs and the corresponding CACTDs are colored by the same colors (light and dark, respectively). (B) Close-up stereo view of the PF74 binding site [small box in (A)]. CANTD and a CACTD of a neighboring subunit bind PF74 (light blue and purple ribbons). H9 is omitted for clarity. PF74 is modeled in a 2.7 Å simulated annealing omit map (σ = 2.5). Black dashed lines indicate interactions within ~4 Å, and red dashed lines indicate H-bond interactions. (C) PF74 conformations in CAPF74 (blue), CAXL-PF74 (PDB ID: 4U0E; PF74 in gray), and CANTD-PF74 (PDB ID: 2XDE; PF74 in magenta). PF74 in PDB ID 4QNB is almost identical to 4U0E and is omitted for clarity. (D) Stereo view of the threefold interface of CAPF74 superposed onto native CA (aligned on residues 1 to 219). Helices H10 of CAPF74 and CA are in blue and yellow, respectively. CA waters are shown as yellow spheres; no waters were present in CAPF74.
Anna T. Gres et al. Science 2015;349:99-103
Published by AAAS