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Results: 3

1.
Figure 1

Figure 1. From: Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3.

Structure of human MRG15 chromo domain. (A) Overall structure. Left panel: secondary structure elements. Right panel: structure of the potential binding pocket for a modified residue. Residues forming the pocket are shown with side chains. (B) Electrostatic surface of the MRG15 chromo domain. The β-barrel core and the C-terminal α-helix form a large surface cleft.

Peng Zhang, et al. Nucleic Acids Res. 2006 December;34(22):6621-6628.
2.
Figure 3

Figure 3. From: Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3.

In vitro binding assays showing that the MRG15 chromo domain can bind to methylated H3K36. (A) GST pull-down assays of the GST-fused MRG15 chromo domain (MRG15N) and the mouse HP1α with the calf thymus histone mixture. The protein samples were analyzed by SDS–PAGE with Coomassie blue staining. The results clearly show that the MRG15 chromo domain can bind to histone H3. (B) Western blot analysis of the GST pull-down samples of the MRG15 chromo domain (MRG15N), the mouse HP1α and the yeast Eaf3p chromo domain (Eaf3pN) with the calf thymus histone mixture. The mouse HP1α binds to H3K9me2 and H3K27me2. The yeast Eaf3p chromo domain binds to H3K36me2 and H3K4me3. The MRG15 chromo domain binds to H3K36me2. GST was used as a negative control. (C) Control experiments showing the specificity of the anti-H3K36me2/3 antibodies. The anti-H3K36me2 antibody has a high specificity with the H3K36me2 peptide and a weak cross-reaction with the H3K36me3 peptide, but no reaction with the unmethylated H3K36 peptide. The anti-H3K36me3 antibody recognizes only the H3K36me3 peptide. (D) In vitro binding assays of the N-terminal His-tagged MRG15 chromo domain with the H3K36me2 and H3K36me3 peptides. The yeast Eaf3p chromo domain (Eaf3pN) was used as a positive control. The results show that the MRG15 chromo domain can bind to both H3K36me2 and H3K36me3 peptides, but not the unmethylated H3K36 peptide.

Peng Zhang, et al. Nucleic Acids Res. 2006 December;34(22):6621-6628.
3.
Figure 2

Figure 2. From: Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3.

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.

Peng Zhang, et al. Nucleic Acids Res. 2006 December;34(22):6621-6628.

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