Figure 2. Sequence and structural features of RIG-I that contribute to duplex RNA recognition. (A) Sequence alignment of DRAs and other SF2 proteins. Notice motifs IIa and Vc (boxed in dotted lines) are not very conserved in amino acid sequence. (B) HEL2i domain juxtaposes with the duplex RNA backbone (PDB codes: 3TMI in green; 2YKG in yellow; 4A36, in magenta). (C) Specialized motifs IIa and Vc recognize the top strand of the duplex RNA (Botton strand or tracking strand is the strand nucleic acid that binds to the SF2α proteins; Top strand is the complementary strand). (D) Possible structural conservation of motif IIa and motif Vc found in DEAD-box RNA family members. Figure shows the aligned structures of DEAD-box protein:ssRNA complexes with duplex RNA (PDB codes: 2J0S, 3I5X, 3G0H and 2DB3). The possible presence of motif IIa and Vc in DEAD-box proteins are labeled in parenthesis.