Figure 2
From: Functional characterisation of a novel class of in-frame insertion variants of KRAS and HRAS
Structural context of VMOS RAS insertions. (A) Sequence alignment on amino acid level from position 50 to 80. The sequences of HRAS and KRAS are identical in the aligned region and labelled as wild type. Duplicated sequence is highlighted once by light red and once by yellow background; novel sequence by light blue and point mutations by red background. Note: This colour coding is irrespective of the genetic rearrangements on DNA level purely based on the amino acid sequence. Elements of secondary structure are displayed above the alignment, with helix α2 in dark blue and N- and C-terminal connecting loops in light blue. The position of Q61 is marked by a red circle. The affected genes are indicated left to the alignment. Case number, Variant Allele Frequency (VAF), and age and sex of the patient are listed right to the alignment. (B) Structure of HRAS in complex with the hydrolysis resistant GTP analogue GppNHp in ribbon representation but with helix α2 and its connecting loops as dark blue backbone trace. Cα-atoms in the backbone trace are shown as colour coded spheres: helix α2, dark blue; connecting loops, light blue; Gln61, red. This region corresponds to switch II. Switch I is highlighted in magenta. Style of representation and colour code is maintained throughout this figure. The likely place of insertion is indicate by an arrow. Dark grey, GppNHp in ball-and-stick representation. (C–E) Structures of HRAS (ribbon representation, dark grey) in complex with SOS acting as GEF (C), RasGAP (D), and the effectors RalGDS (E, left), PI3K (E, middle) and SOS (E, right) (space filling representation). Nucleotides are shown in ball-and-stick representation in black: GDP•AlF3 (D) and GppNHp (E). The ubiquitin folds of RalGDS and PI3K mediating the interaction with RAS are coloured in orange. See Supplementary Fig. 1B for RAS in complex with the ubiquitin folds of the effectors RAF38, PLCε39, and Nore140. Note: The orientation of RAS is different in each panel, but identical for all complexes in (E) to allow for a free view of the interaction surface. See Supplementary Fig. 1A for a set of figures in identical orientation. Figures were generated base on the pdb database entries 5p2115, 1dbk32, 1wq116, 1lfd41, 1he842, and 1nvv22 by use of the programs molscript43 and raster3D44.
