The activated form of vinculin primarily localizes to FAs [ 17] where the binding sites for its many partners, including talin and α-actinin (which bind to the head domain), VASP, vinexins, ponsin, and Arp2/3 (which bind to the neck region), and paxillin, F-actin, and PIP2 (which bind to the tail domain) are exposed [ 18].
The N-terminus of EF-3 has a HEAT domain which is absent in RbbA (Figure S3B) and was shown by Cryo-EM analysis to bind to the head of the 80S and reach the L1 stalk of the yeast 60S ribosomal subunit E-site, suggesting that it may participate in release of deacyl-tRNA from ribosomes during each step of elongation [39].
Further biochemical investigations (Lu et al, 2007; Tsai et al, 2007) subsequently supported this contention and, furthermore, indicated that residues 1 128 of XLF bind to the head domain (residues 1 119) of XRCC4 (Deshpande and Wilson, 2007).
Furthermore, differences in connect position mean differences in internal strain, as the number of free neck linker amino acids, which do not bind to the head and act as a spring, is different for each connect position (see Supplementary Results for details).
We chose position 328, the halfway position of the neck linker to minimize the effect of free amino acids from the neck linker that do not bind to the head, and thus maximized the effect of the three different carbon chains: AMAS, EMCS and KMUS.
The yeast 80S structure was also solved in the presence of STM1, a translation repressor protein, that binds to the head region of the 40S and blocks mRNA entry and binding of tRNA to the A- and P-sites (Rabl et al., 2011).
The JL2 Fab binds to the head of SCARB2 (Domain III) at a perpendicular angle with helices α2, α5, and α14 involved in the interaction.
The complex structure revealed that JL2 binds to the head of SCARB2 (Domain III) at an approximately perpendicular angle via the three helices of α2, α5, and α14 (Fig. 4A).
When a subsequent ATP binds to the head, the head again diffuses along the actin filament.
Furthermore, we previously showed that not only Nse4 but also Nse3 (as well as Nse5 and Nse6 in S. pombe) bound to the head domain of Smc6 ([13]; K. Bednarova unpublished data).
Kinesin lacks the rigid lever arm, but upon ATP binding to the head, a conformational change in the neck linker occurs during which the neck linker binds to the head (termed 'docking'docking
