Table 1.
Data Collection and Refinement Statistics
Figure 1.
Surface Representation of the Complete Archaeal RNA Polymerase from S. shibatae
The overall architecture of the RNAP is shown with the different subunits colour-coded as illustrated in the Subunit Nomenclature (below). The newly located structural elements are labelled.
Figure 2.
Newly Identified Subunits and Located Subdomains
(A) Ribbon representation of the clamp-head domain in Rpo1N (light grey); C98, C101, and C146 as green stick; and Zn ion as a cyan sphere. On the right, sigmaA-weighted 2Fo-Fc electron density countered at 1σ (as a blue mesh) corresponding to the Zn2+ and surrounding cysteines (arbitrary view).
(B) Cartoon representation of the jaw domain in the Rpo1C subunit.
(C) Cartoon representation of the entire Rpo8 subunit. On the right, sigmaA-weighted 2Fo-Fc electron density countered at 1.2σ of a structural detail.
(D) Stereo view of the sigmaA-weighted 2Fo-Fc map electron density (contoured at 1.1σ) correspondent to the HTH motif of the Rpo13 subunit (as orange ribbon with N and C labelling the N- and C-termini). The inset shows some side chains (as sticks) fitting density.
Figure 3.
Binding locus of Subunit Rpo13
(A) Electrostatic surface representation (blue positive, red negative, and white neutral) with Rpo13 as orange ribbon (C labels the C-terminus) and semitransparent surface.
(B) Stereo view of the docking region of Rpo13 (orange), in light-magenta Rpo5 and in grey Rpo1 with the eukaryotic Rpb5 (violet) and Rpb1 (plum; PDB entry 1WCM) superimposed; rmsd 2.4 Å for 1,129 Cα equivalences.
(C) Archaeal Rpo13, Rpo5, and Rpo1 as (B) with the bacterial β′ from the T. aquaticus RNAP core structure (turquoise; PDB entry 1I6V) superimposed; rmsd 3.4 Å for 748 Cα equivalences. The two spheres mark the insertion region 1,377–1,420 in the bacterial β′ that spatially correlates with the archaeal subunit Rpo13. Superimpositions were carried out using the Structure Homology Program [44].
Figure 4.
Ellipsoid Representation of the Thermal Motions of the Entire RNAP
B ranges from Bmin = 40 Å2 (dark-blue) to Bmax = 233 Å2 (red) values obtained by normal mode analysis [27]. Subunits Rpo4/7 are highly mobile, whereas the inset highlights the catalytic site as a rigid frame. All figures in this article were generated in Pymol [45].
Figure 5.
Archaeal Preinitiation Complex Model
(A) Secondary structure elements of Rpo13 model (orange) aligned with the amino acid sequence (below), yellow secondary structure prediction (Protein Prediction [19]) with reliability histogram (0 = low to 9 = high), and graph of disorder prediction (RONN [18]).
(B) Left, overall architecture with RNAP, TBP-TFB-DNA modelled as described in the main text, represented as a surface and coloured as in the key. Right, enlarged view of the TBP-TFB-DNA complex with the DNA wrapping the RNAP from the back (as viewed from left to right) with the downstream DNA in the entry channel close to Rpo13.
(C) Stereo view of the two ordered helices (α1 and α2) of Rpo13 and DNA with the C-terminal end proximal to the DNA major groove at nucleotide +8.
(D) Cartoon representation of the model of action of Rpo13 during polymerase activity (elements described in the key); star (yellow) marks the catalytic site, circle (grey) the bridge helix, and arrow (black) the direction of DNA translocation. The nucleic acid arrangement at the fork reflects the RNAP II elongation complex structure [46]. The location and orientation of Rpo13 α3 onto the DNA are speculative.