Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography
Figure 5
Sequence alignment of VP60s of representative RHDV isolates and location of variation regions on the capsomer surface.
(A) Multiple sequence alignments of VP60s among six genetic groups of RHDV isolates according to Nystrom, K. et.al. [20]. The alignment is just shown for the P2 sub-domain region for residues from 301 to 480. The GeneBank accession numbers for those isolates shown are JF438967 (G1), Z24757 (AST/89), Z49271 (RHDV-AST89), FR823355 (G2), AF231353 (NZ), FR823354 (G3), AJ535092 (95-05FR), AJ535094 (G4), Y15424 (Frankfurt), AJ006019 (Rainham), AM085133 (G5), Y15427 (Wriezen), AY926883 (Ireland12), AY928269 (Ireland19), AJ969628 (G6), DQ069280 (whn/China/01/2005), AF453761 (China/Harbin/TP), DQ205345 (JX/CHA/97), AJ303106 (00-ReuFR), AY269825 (NJ/China/1985), DQ530363 (China-Yingling(YL)), and DQ069281 (whn/China/02/2005). The seven variation regions (V1–V7) that distinguish these isolates are highlighted in yellow. Sequence alignments were performed and plotted using Chimera [39]. (B) Locations of variation regions on the RHDV capsomer surface. The degrees of sequence conservation based on the multiple sequence alignments in (A) are mapped onto the surface of the RHDV capsomer (shown in top view on the left). The most highly conserved regions (between 80 and 100% conservation) are shown in colors varying from white to cyan and then green, whereas less conserved regions (from 80 down to 43%) are represented in shades from white to violet. The seven variation regions in each of the two P2 sub-domains are indicated by dashed black ellipses and are labeled in gold in one monomer and blue in the other. The right panel shows a view of the variation sites from a different angle and three putative binding sites for HBGAs are highlighted with dashed red circles and labeled C1, C2 and C3.