Fig. 2: Structure of the AR9 nvRNAP promoter complex.
From: Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase
a Ribbon diagram of the crystal structure of the AR9 nvRNAP in complex with a forked oligonucleotide containing the AR9 late promoter P077 in its 3′-overhang region (AR9 nvRNAP-Pro-Xray). Structural elements that are either unique to the AR9 nvRNAP or common to all RNAPs are labeled and color coded. The βN gp105 subunit is semitransparent for clarity. b Schematic of the two oligonucleotides that bound to one AR9 nvRNAP molecule resulting in a transcription bubble-like structure. Bases disordered in the crystal structure are rendered semitransparent. Bases in purple boxes interact with the protein. The dashed lines indicate that the sequence of the non-template strand which is in-register with the promoter is partially complementary to it. c, d Structure of the catalytic centers of the AR9 nvRNAP and E. coli RNAP-σS (PDB code 5IPM21). Here and elsewhere, TSS stands for the transcription start site. The 2.4 region of σS, which is not present in gp226, is rendered semi-transparent. The E. coli RNAP-σS structure contains a short RNA product that is not shown for clarity. A part of the DNA non-template strand in the E. coli RNAP-σS structure is semitransparent for clarity.
