Figure 7
From: Determination of RNA polymerase binding surfaces of transcription factors by NMR spectroscopy
Model for the binding of NusA-NTDΔ to elongating RNAP.
(a) NusA-NTDΔ (cartoon and surface representation, pink) is docked to elongating TtRNAP (PDB ID: 2O5I, surface representation). Residues in NusA-NTDΔ that are affected by RNAP binding are highlighted in yellow and two amino acids on either side of an affected Ile/Leu/Val residue are colored in light pink unless they were unaffected Ile/Leu/Val residues. α1, light grey; α2, dark grey; β, blue; β′, pale green; ω, olive; β flap tip helix, teal; RNA, orange; DNA, black. (b) Binding of exiting RNA by NusA. The orientation of NusA-NTDΔ is the same as in (a), the position of TmNusA-SKK was modeled by superposing TmNusA-NTD (PDB ID: 1L2F) on NusA-NTDΔ. RNA was taken from the MtNusA-SKK:RNA complex (PDB ID: 2ASB). Representation of NusA-NTDΔ, TtRNAP and nucleic acids as in (a). The β′ dock domain is highlighted in green. TmNusA-SKK (brown) is in surface representation with residues affected by RNA binding highlighted in red according to Schweimer et al.4. The grey line shows a possible path of exiting RNA, the estimated base numbers are indicated.
