RNA polymerase I-Rrn3 complex at 4.8 Å resolution

Abstract

Transcription of ribosomal DNA by RNA polymerase I (Pol I) requires the initiation factor Rrn3. Here we report the cryo-EM structure of the Pol I-Rrn3 complex at 4.8 Å resolution. The structure reveals how Rrn3 binding converts an inactive Pol I dimer into an initiation-competent monomeric complex and provides insights into the mechanisms of Pol I-specific initiation and regulation.

Figure 1. Cryo-EM structure of the Pol I–Rrn3 complex at 4.8 Å resolution.

(a) Overview of the cryo-EM density (mesh) with fitted atomic structures (ribbon models) of Pol I (subunits in previously used colors6) and Rrn3 (green). The view is from the back. (b) Partial cleft closure observed by superposition of the expanded dimeric Pol I crystal structure (black, PDB-code 4C2M) and the partially contracted, Rrn3-bound form (orange). The A135 subunits were superimposed. (c) The A12.2 C-terminal domain shows cryo-EM density and is well defined in the Pol I–Rrn3 complex structure, although the catalytic loop is mobile. (d) Rotation of the A12.2 C-terminal domain compared with the position observed in the free Pol I structure. The nearby bridge helix is partially rewound. (e) Superposition of the free Pol I crystal structure onto the Pol I–Rrn3 complex structure reveals that the connector (space filling, blue) would clash with the three N-terminal HEAT repeats of Rrn3 (green).

Figure 2. Details of the Pol I–Rrn3 interface.

(a) Four interfaces between Rrn3 and Pol I. Schematic representation (left) and cartoon model (right) of Rrn3 HEAT repeats and their Pol I—interaction interfaces I–IV are labeled (see text). The flexible Rrn3 loop 551–580, which contains lysine 558, and its crosslinked interaction partners K329 (in AC40) and K582 (in A190) are indicated. The view is from the back of polymerase. (b) Bending of Rrn3 towards Pol I upon Pol I–Rrn3 complex formation. A hinge between the N- and C-terminal parts of Rrn3 enables rotation of the C-terminal region towards Pol I and tight interaction with the AC40/AC19 heterodimer. (c) Interface I viewed from the front. All eight serine residues (orange) that compose the ‘serine patch' of Rrn3 (ref. ; space filling, green) are located in the interface and face the stalk. (d) Interface III viewed from the back. A second interface is constructed between the A190 dock domain and the Rrn3 helices α10 and α12 as well as rearranged loop between α12 and α13. The Rrn3-interacting A190 helix α12a and the subsequent loop are specific to Pol I.