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. Author manuscript; available in PMC: 2018 Jan 1.
Published in final edited form as: Trends Biochem Sci. 2016 Nov 5;42(1):72–84. doi: 10.1016/j.tibs.2016.10.003

Figure 4. Models of the combined RAG1 domains ZDD and NBD bound to RSS nonamers.

Figure 4

(A) Ribbon diagram of the ZDD structure in two orientations, generated using PDB ID: 1RMD. The ZDD subunits are in blue with the ZFA regions in purple. The zinc ions are light yellow spheres. (B) Ribbon diagram of the structure consisting of an NBD dimer bound to 2 RSS nonamers is shown in two orientations, generated using PDB ID: 3GNA. The NBD subunits and RSS nonamers are in green and orange, respectively. (C) Docked model of the structures in panels A and B are shown. The N-termini of NBD and C-termini of ZDD are shown as green and purple spheres, respectively. (D) Model of the ZDD (PDB ID: 1RMD) docked to the non-symmetrized PC complex (PDB ID: 3JBW), in which the relative orientation of the ZDD to the RSS nonamers is the same as in panel C. Core RAG2 subunits are in purple, core RAG1 subunits are in light and dark green, and non-core RAG1 ZDD subunits are in cyan and light blue. The positions of core RAG2, non-core RAG1 ZDD, core RAG1 NBD, and the region containing the remaining core RAG1 modules (DDBD-CTD) are as indicated. The 12-RSS and 23-RSS are pink and orange, respectively. The two-fold axis of symmetry in the ZDD was modeled to coincide with the two-fold axis for the NBD dimer. Ribbon diagrams were produced using The PyMOL Molecular Graphics System, Version 1.6.9, Schrödinger, LLC.