Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCR[zeta] fragments

HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling [zeta] subunit of the T-­cell receptor (TCR[zeta]). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nef_core) in complex with two different TCR[zeta] fragments are described. The structure of SIVmac239 Nef_core bound to the longer TCR[zeta] polypeptide (Leu51-Asp93) was determined to 3.7 Å resolution (R_work = 28.7%) in the tetragonal space group P4₃2₁2. The structure of SIVmac239 Nef_core in complex with the shorter TCR[zeta] polypeptide (Ala63-Arg80) was determined to 2.05 Å resolution (R_work = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P2₁2₁2₁. The reduction in crystal space-group symmetry induced by the truncated TCR[zeta] polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, -l) and a and b unit-cell parameters that were nearly identical predisposed the P2₁2₁2₁ crystal form to pseudo-merohedral twinning.