Extended Data Fig. 8: Structural modeling and cryoEM analysis of HYPK bound to NatA on the RNC-NAC complex.

(a-d) HYPK H2 in inhibitory conformation would clash with bound H2 of NACα. In (a), the model of HYPK from NatA-HYPK complex (PDB 6C95) is superimposed on the model of NatA/E from the quaternary RNC-NAC-NatA/E-MetAP1 complex. Models were aligned by Naa15, only HYPK from the isolated NatA-HYPK complex is displayed. (b) shows the model of NAC-NatA/E from the quaternary RNC-NAC-NatA/E-MetAP1 complex. (c) shows the model of HYPK from NatA-HYPK complex (PDB 6C95) superimposed on the model of NAC-NatA/E from the quaternary RNC-NAC-NatA/E-MetAP1 complex. The binding site of HYPK H2 in its inhibitory conformation on Naa15 in part overlaps with that of H2 of NACα, when NatA/E is recruited to the ribosome. (d) shows a model of NatA/E-HYPK-NAC from the quaternary complex with HYPK. The N terminus of HYPK is remodelled upon recruitment to the ribosome by NAC. The flexible linker connecting NACα H2 and UBA and displaced HYPK N terminus are shown as yellow and purple dotted lines, respectively. (e-j) Comparison between cryo-EM maps of quaternary complexes with and without HYPK. e-g, details of the locally refined cryo-EM map of the quaternary complex showing the front view of the quaternary complex (e), a segment of Naa15 with NACα UBA (f), and MetAP1 (g). h-j, details of the locally refined cryo-EM map of the quaternary complex with HYPK showing the front view of the complex (h) and a segment of Naa15 with NACα UBA and HYPK UBA (i). A detail of a homogeneously refined map, lowpass filtered to 6 Å resolution, shows how NACα-H2 connects to the globular domain of NAC (j). The maps are displayed as solid surfaces (e, h) or as semi-transparent surfaces superimposed on models of the complexes (f-g, i-j). Colors are the same as in Fig. 1e, with MetAP1 in blue-grey and HYPK in purple.