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. Author manuscript; available in PMC: 2015 Dec 24.
Published in final edited form as: Cell. 2015 Nov 5;163(5):1138–1152. doi: 10.1016/j.cell.2015.10.055

Figure 4. RSS Recognition at the Heptamer and the Spacer.

Figure 4

(A) Electrostatic surface of the RAG dimer from the symmetrized SEC model with bound RSSs (orange) and coding end mimics (magenta) in ribbons. The cyan oval shows the RAG surface for one RSS.

(B) Side and bottom views of the RAG dimer displayed as molecular surfaces with bound DNAs displayed in ribbons. For the reference RSS, nucleotides with base recognition by RAG are highlighted in blue, whereas others are shown in orange. Domains involved in RSS interactions are colored as in Figure 1A, except that one DDBD at the bottom view is shown in blue to distinguish it from the neighboring DDBD. Two RAG2 molecules are shown in gray. A prime symbol is added to domain names for the symmetric subunit that interacts with the reference RSS.

(C) Top and side views of RAG1 regions (magenta) that are in contact with the heptamer DNA. RSSs are colored as in (B). RAG2 subunits are omitted.

(D) A bound RSS colored as in (B) superimposed with an ideal B-form DNA (light blue), showing the widening of the minor groove. The α23-α24 loop inserted into the minor groove of the RSS is highlighted in magenta.

(E) Schematic depiction of the detailed interactions between RAG and the RSS. RAG1 residues from one and the symmetric subunits are displayed as cyan and lemon green ovals, respectively. These ovals are bounded in blue lines, no lines, and red lines, respectively, for side-chain, main-chain, and side- and main-chain interactions. Slate, green, magenta, and gray arrows indicate interactions at the major groove, minor groove, flipped base, and the backbone. Heptamer bases that have multiple contacts with RAG are highlighted in red, and those with a single contact are in pink.

(F) Detailed interactions between RAG and the heptamer DNA. Direct base interactions are highlighted in magenta for the protein and in green for the bases. Potential interactions are displayed as yellow dashed lines.

(G) Superimposed apo-like RAG crystal structure (magenta and red, PDB: 4wwx) and SEC (lemon green and cyan) at the heptamer-binding site. One RAG1 subunit (red and cyan) is aligned, showing the different orientations of the symmetric RAG1 (magenta and lemon green), especially at the β4-β5 loop that was disordered in the crystal structure, and the α23-α24 loop.

(H) Detailed interactions between RAG and the flipped C1 of the heptamer DNA.

See also Figure S4.