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. 2017 Oct 16;6:e30244. doi: 10.7554/eLife.30244

Figure 2. Crystal structure of Kl Kap123 in complex with H31–28-NLS.

(a) Crystal structure of full-length Kl Kap123 in the presence of H31–28-NLS (green stick model, 1-ARTKQTARKSTGGKAPRKQLASKAARK-28) with two lateral views (180° rotation). The two lysine-binding pockets located at the inner curvature of Kap123 are marked with red (first lysine-binding pocket) and blue (second lysine-binding pocket) dashed circles. Residues 12–17 and 21–26 of H31–28-NLS (chain B) are ordered and visible in the structure. The two lysine residues (H3 K14 and K23) that bind to these lysine-binding pockets of Kap123 are colored red. (b) Schematic view of Kl Kap123 in complex with H31–28-NLS. The residues and HEAT repeats that participate in organizing two lysine-binding pockets are described. (c) The first lysine-binding pocket of Kl Kap123. K14 of H31–28-NLS forms hydrophobic (Y926) and electrostatic/hydrogen bond (N980, E1016, and E1017) interactions with Kap123 through repeats 20–22. (d) The second lysine-binding pocket of Kl Kap123. K23 of H31–28-NLS makes hydrophobic (Y512) and electrostatic/hydrogen bond (D465, S505, S509, and N556) interactions with Kap123 through repeats 11–13. (e) Top view of Kl Kap123 in complex with H31–28-NLS. Two lysine-binding sites are distally located and the middle region of H31–28-NLS does not make any specific contacts with Kap123.

Figure 2.

Figure 2—figure supplement 1. Multiple sequence alignment of Kap121 and Kap123 in budding yeast.

Figure 2—figure supplement 1.

Primary sequences of K. lactis Kap123, S. cerevisiae Kap123, K. lactis Kap121 and S.cerevisiae Kap121 were aligned using Clustal Omega (Adams et al., 2010). The illustration for the alignment was generated with Jalview using default settings (Waterhouse et al., 2009). Highly conserved residues are shown in purple. The secondary structure identified from the K. lactis Kap123 crystal structure is shown above the sequence with the corresponding HEAT repeats with inner (cyan) and outer (blue) helices. Linker regions are colored in grey. The H23 insert region (Figure 1—figure supplement 1), a unique feature of K. lactis Kap123, is also indicated above the sequence. K. lactis Kap123 residues that form the first lysine-binding pocket (solid red circle) and the second lysine-binding pocket (solid blue circle) in the Kap123-H31-28-NLS complex are marked below the sequence accordingly. Residues involved in the H3-NLS peptide backbone interaction near the first lysine-binding pocket (open red circle) and the second lysine-binding pocket (open blue circle) in the Kap123-H31-28-NLS complex are also indicated below the sequence.
Figure 2—figure supplement 2. The Composite omit map (1.0 σ contour level) of the Kap123-H31-28-NLS complex.

Figure 2—figure supplement 2.

The composite omit map of the first lysine-binding pocket (a) and the second lysine-binding pocket (b) of Kap123. The omit map was calculated in the absence of H3 peptide using Program Composite omit map in the PHENIX package (Sievers et al., 2011).
Figure 2—figure supplement 3. H31–28-NLS peptide backbone interactions in the Kap123-H31–28-NLS complex.

Figure 2—figure supplement 3.

(a) H31–28-NLS peptide backbone interactions near the first lysine-binding pocket. Kap123 residues near the first lysine-binding pocket (repeats 19–21; E889, N923, and R976) form multiple hydrogen bond interactions with the peptide backbone of H31–28-NLS (stick model, green). (b) H31–28-NLS peptide backbone interactions near the second lysine-binding pocket. Kap123 residues near the second lysine-binding pocket (repeats 11–14; E469, R562, and N601) form multiple hydrogen bond interactions with the peptide backbone of H31–28-NLS (stick model, green). H3 K14 and K23 associate with the first and second lysine-binding pocket, respectively (red). Unstructured regions of H31–28-NLS are shown as green dashed lines.
Figure 2—figure supplement 4. Structural comparison of Kap123-H31-28-NLS and Kapβ2-H31-47-NLS complexes.

Figure 2—figure supplement 4.

(a) The side-views of both Kapβ2-H31-47-NLS (yellow, PDB ID: 5J3V) (Soniat and Chook, 2016) and Kap123-H31-28-NLS complexes. H3-NLS peptides in both structures are colored green with stick and cartoon model. (b) The conformation of H3-NLS peptides within the Kapβ2-H31-47-NLS and Kap123-H31-28-NLS structures. Residues 12–27 and 12-18/22-25 of histone H3 are only visible in Kapβ2-H31-47-NLS and Kap123-H31-28-NLS, respectively. Key lysine residues participating in Kap association (K14 in Kapβ2-H31-47-NLS and K14/K23 in Kap123-H31-28-NLS) are colored red. Residues 19–21 of H3-NLS in Kap123-H31-28-NLS are disordered and displayed as dashed line.