Fig. 2: RPAP2 binding is incompatible with transcription initiation and elongation.
From: Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2
a Superposition of the Pol II-RPAP2 structure onto the Pol II elongation complex (PDB: 5FLM) reveals that RPAP2 would clash with downstream DNA (blue/cyan). b Superposition of the Pol II-RPAP2 structure onto the Pol II pre-initiation complex (PDB: 5IYA) reveals that RPAP2 would clash with downstream DNA (blue/cyan). c Binding competition assays using the preformed Pol II–RPAP2(1–215) complex (peak 4) show that RPAP2 is displaced from Pol II upon formation of an elongation complex (peak 1) or a pre-initiation complex (peak 2) but cannot be displaced by double-stranded promoter DNA (peak 3). Chromatograms show the formation of complexes and the relevant peak fractions used for SDS–PAGE and western blot analysis are indicated. Peaks for free nucleic acids are indicated by NA and vertical dashed lines show the elution peak of free RPAP2(1–215). A representative western blot analysis of the same peak fractions using anti RPAP2 (Thermo Fisher #PA5-61244) and anti RPB3 (BETHYL #A303-771A) antibodies are shown. Please refer to Supplementary Fig. 5 for source data of western blots.
