LIR motif consensus and structural determinants of LIR–ATG8 interactions. LIR motif consensus and structural determinants of LIR–ATG8 interactions. (A) Surface representation of LC3B bound to the p62-LIR peptide (top left), yeast Atg8 bound to the Atg19-LIR peptide (top right), GABARAP-L1 bound to the NBR1-LIR peptide (bottom left) and LC3C bound to the NDP52-LIR peptide (non-canonical LIR-motif) (bottom right). The hydrophobic pockets (HP1 and HP2) of LC3B, Atg8 and GABARAP-L1 as well as the hydrophobic patch of LC3C are indicated in bright yellow. The amino acids (yellow) of the different LIR peptides that bind in the pockets are shown as well as the amino acids (red) that interact with basic residues of the ATG8 proteins (blue). (B) Ribbon diagram of LC3B with the N-terminal arm (blue) and the Ubl domain (gray). The bound p62-LIR peptide is depicted in red. Amino acids D337 and D338 in the p62-LIR peptide interact with the basic residues R10 and R11 in the N-terminal arm of LC3B. Amino acids W340 and L343 in the p62-LIR peptide binding to hydrophobic pockets in LC3B are also indicated. (C) Sequence logos that are a graphical representation of amino acid residues as stacks at each position in multiple sequence alignments of LIR motifs. The overall height of the stack indicates the sequence conservation at that position, whereas the height of symbols within the stack indicates the relative frequency of each amino at that position. The sequence logos were created on the basis of 42 verified LIR motifs (upper panel) and were split into 22 W-type LIRs (middle panel) and 15 F-type LIRs (lower panel). The analysis of these 42 LIRs (33 of which are published, see supplementary material Table S1) confirms the core consensus sequence [W/F/Y]xx[L/I/V], in which alternative letters are placed in square brackets with a solidus between them. Only five LIRs have Tyr (Y) at the aromatic position binding to the HP1 pocket. W-type LIRs prefer Leu (L) in HP2 (13 out of 22). Such a preference is not seen among the 15 F-type LIRs, in which I, L and V are similarly distributed. F-type LIRs have a significantly higher average number of acidic residues than W-type LIRs. The average number of E, D, S, or T in the three positions N-terminal to the core hydrophobic residue (positions X−1 to X−3) is 1.7 and 2.5 for W- and F-type LIRs, respectively. The Seq2Logo-1.0 server (http://www.cbs.dtu.dk/biotools/Seq2Logo-1.0/) was used with Kullback-Leibler logo type and Hobohm1 clustering (threshold 0.63 and 0 weight on prior pseudo counts) (Thomsen and Nielsen, 2012). Åsa Birna Birgisdottir et al. J Cell Sci 2013;126:3237-3247 © 2013. Published by The Company of Biologists Ltd