Fig. 3.

Structural basis for the recognition of H3K27me3 by JMJ13. a H3R26 and H3S28 form hydrogen bonds (dashed silver lines) with JMJ13 Asp236 and Asp296, respectively. The prolyl ring of H3P30 stacks with the phenyl ring of JMJ13 Phe179. b The superposition of JMJ13-α-KG complex (in cyan) and JMJ13-NOG-H3K27me3 complex (in green) shows that the binding of H3K27me3 peptide induces a significantly conformational change of the side chain of Phe179. The SIGMAA weighted 2Fo-Fc maps at 1 sigma level of the Phe179 in the two complexes are shown in meshes. c The methyl groups are specifically anchored by surrounding CH–O hydrogen bonds. The nickel ion is coordinated by NOG, a water molecule, and surrounding residues. d In vitro H3K27me3 demethylation activity assay of MBP-tagged JMJ13CD and its mutants showing the mutations of key residues involved in peptide binding and catalysis are decreasing the activity of JMJ13. The MBP protein was used as a negative control. The percentages of the product peptide are shown as means ± SD (n = 3). Green dots denote the individual data points. Source data are provided as a Source Data file