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. 2006 Nov 28;34(22):6621–6628. doi: 10.1093/nar/gkl989

Figure 2.

Figure 2

Comparison of the MRG15 chromo domain with representative chromo and chromo-like domains. (A) Sequence comparison of the chromo domains between MRG15 and its homologues in other species. Hs, Homo sapiens; Mm, Mus musculus; Dm, Drosophila melanogaster; Sp, Schizosaccharomyces pombe; Sc, Saccharomyces cerevisiae; At, Arabidopsis thaliana; and Ce, Caenorhabditis elegans. Strictly conserved residues are highlighted in shaded red boxes and conserved residues in open red boxes. The secondary structure of the MRG15 chromo domain is placed on top of the alignment. (B) Structure-based sequence alignment of the MRG15 chromo domain with representative chromo, Tudor and PWWP domains. The secondary structure for the first member of each group is placed on top of the alignment. Dm_MOF: the dMOF chromo barrel domain, PDB code 2BUD; Mm_MOF: the mouse MOF chromo barrel domain, PDB code 1WGS; Mm_HP1b: the mouse HP1β chromo domain, PDB code 1GUW; Dm_HP1: the Dm HP1 chromo domain, PDB code 1KNA; Dm_Pc: the Dm Pc chromo domain, PDB code 1PDQ; Sp_CLR4: the Sp CLR4 chromo domain, PDB code 1G6Z; Hs_SMN: the human SMN Tudor domain, PDB code 1G5V; Mm_53BP1: the mouse 53BP1 Tudor domain, PDB code 1XNI; Aa_NusG: the Aquifex aeolicus transcription factor NusG Tudor domain, PDB code 1M1G; Mm_Dnmt3b: the mouse Dnmt3b PWWP domain, PDB code 1KHC; Hs_HDGF: the human HDGF domain of hepatoma-derived growth factor (HDGF)-related protein, PDB code 1RIO; Sp_SPBC215: the Sp protein SPBC215 PWWP domain, PDB code 1H3Z; Mm_HRP: the PWWP domain of mouse HDGF-related protein 3, PDB code 1N27. The stars indicate conserved residues that form the hydrophobic pocket in the HP1/Pc chromo domains and the triangle indicates the residue that occupies in part the hydrophobic pocket. (C) Structural comparison of the MRG15 chromo domain with the dMOF and HP1 chromo domain, the HP1 chromo shadow domain, the SMN Tudor domain and the Dnmt3b PWWP domain. Residues forming the hydrophobic pocket are shown with side chains and the bound peptides in the HP1 chromo domain complex and the HP1 chromo shadow domain complex are shown in magenta. (D) Superposition of the MRG15 chromo domain (red), the dMOF chromo barrel domain (magenta), the HP1 chromo domain (yellow), the SMN Tudor domain (cyan) and the Dnmt3b PWWP domain (green). The bound histone H3 peptide in complex with the HP1 chromo domain is shown in blue.