File:GE23077-binds-to-the-RNA-polymerase-i-and-i+1-sites-and-prevents-the-binding-of-initiating-elife02450f005.jpg

English: (A) Crystal structure of RPo-ATP-CMPcPP: crystallographic data and refinement statistics. (B) Crystal structure of RPo-ATP-CMPcPP: electron density and model. Green mesh, mFo-DFc omit map for ATP and CMPcPP:Mg2+(II) (contoured at 2.5σ); pink sticks, ATP and CMPcPP; red ribbon, DNA template strand; gray ribbon, RNAP bridge helix; upper and lower violet spheres, Mg2+(I) and Mg2+(II). (C) Crystal structure of RPo-ATP-CMPcPP: contacts between RNAP and initiating NTPs (stereodiagram). Gray ribbon, RNAP bridge helix; gray sticks, RNAP carbon atoms; continuous red sticks, DNA atoms; pink sticks, ATP and CMPcPP carbon atoms; individual red sticks, oxygen atoms; individual blue sticks, nitrogen atoms; red spheres, water molecules; upper and lower violet spheres, Mg2+(I) and Mg2+(II). Blue dashed lines, H-bonds; orange dashed lines, coordinate-covalent bonds. (D) Crystal structure of RPo-ATP-CMPcPP: contacts between RNAP and initiating NTPs (schematic summary). Red dashed lines, H-bonds; orange dashed lines, coordinate-covalent bonds; blue arcs, van der Waals interactions; W, water molecule; underlined residues, GE-contacting residues in RPo-GE. (E) Superimposition of crystal structures of RPo-GE and RPo-ATP-CMPcPP: inferred steric clash between GE and initiating NTPs. Blue mesh, blue sticks, red sticks, and gray ribbon: mFo-DFc omit map for GE, atomic model for GE, DNA template strand, and RNAP bridge helix from RPo-GE (Figure 4). Pink sticks and violet spheres: ATP, CMPcPP, Mg2+(I), and Mg2+(II) from RPo-ATP-CMPcPP. (F) Crystal structure of RPo-GE plus ATP and CMPcPP: crystallographic data and refinement statistics. (G) Crystal structure of RPo-GE plus ATP and CMPcPP: electron density and model. Blue mesh, mFo-DFc omit map for GE (contoured at 2.7σ); blue sticks, GE; green mesh, mFo-DFc omit map for NTP triphosphate:Mg2+(II) in RNAP E site (contoured at 2.7σ); pink sticks, NTP triphosphate; thin pink sticks, NTP sugar and base (projected); red ribbon, DNA template strand; gray ribbon, RNAP bridge helix; upper and lower violet spheres, Mg2+(I) and Mg2+(II). See Figure 5—figure supplement 1.