Figure 1.
Domain structure and functional overview of the Ski/Sno proteins.
Panel A. Schematic representation of the Ski/Sno family of proteins with the conserved domains colored. The family includes the full-length SnoN and splice variants from the sno gene: SnoN2 with 46 aa deletion in the C-terminal region; SnoA, which carries a shorter and unique C-terminal sequence (grey) compared to SnoN; and SnoI, covering only aa 1–399. Human Ski and the v-ski protein of the Sloan Kettering virus are added for comparison. Panel B. Simplified overview of Ski and SnoN involvement in Smad-regulated TGF-β signaling. Ski and Sno proteins can act as bridges between the Smad complex and the N-CoR/mSin3A/HDAC1 repressor complex.
Figure 2.
The SnoN-DHD structure and surface charge comparison.
Panel A: Ribbon representation of SnoN-DHD. Panel B: Comparison between electrostatic surfaces of SnoN-DHD (chain A), Ski-DHD and DACHbox-N. Molecular surfaces are colored according to electrostatic potentials with maximum color potential set to ±5 kT/e. SnoN-DHD, Ski-DHD (PDB 1SBX) and DACHbox-N (PDB 1L8R) are in the same orientation as in Figure 2A. Electrostatic potential was calculated with the program ICM-Pro v.3.7-1e [29] using the REBEL (rapid-exact-boundary-element) method.
Figure 3.
Conserved regions in SnoN-DHD.
Panel A: Sequence alignment between human SnoN-DHD and five orthologous proteins. The sequence of SnoN-DHD corresponds to the protein fragment used in structural determination. The Genbank ID of the five orthologous sequences are: Danio rerio (gi:190338009), Mus musculus (gi:113205055), Nasonia vitripennis (gi: 156550231), Apis mellifera (gi: 110748778), and Aedes aegypti (gi: 157124676). Secondary structure elements and numbering of SnoN-DHD are depicted above the alignment. Alignment was generated by ClustalW [41] and colored by ESPript [40]. Panel B: Conserved residues on the surface of SnoN-DHD. The molecular surface of SnoN-DHD is colored according to the sequence conservation from the alignment in Fig 3A. Residues are colored in red and orange if they are strictly conserved in six or five sequences, respectively. Yellow and pale yellow represent residues that are similar in six and five sequences, respectively. Other residues are colored in white. SnoN-DHD is in the same orientation as in Fig 2A. Panel C: Conserved groove on the surface of SnoN-DHD. Structure of SnoN-DHD is represented in ribbon mode. The molecular surface of the conserved groove mentioned in the text is displayed and colored in light blue. It is composed of the following residues: Leu167, Pro168, Gln169, Leu171, Asn172, Ser173, Leu 180, Ile183, Asn184, Ile210, Leu211, Pro212, Ala215, Ser217, Cys218 and Gly219. The position of these residues on the surface is indicated by their corresponding one-letter label.
Figure 4.
Conformational changes among the SnoN-DHD monomers.
Panel A: Superposition of the twelve monomers of SnoN-DHD present in the asymmetric unit (stereo view). Chains A, B, C, D, E and G are colored in yellow, chains F, I, K and L in blue, and chains H and J in green. The red, orange and violet dots represent the location of Arg176, Tyr191 and Phe213, respectively. Panels B–D: Side-chain conformational changes of Arg176, Tyr191 and Phe213.
Figure 5.
Open and tight conformation of SnoN-DHD: molecular surface representation.
Panel A: SnoN chain C. Backbone of SnoN-DHD chain C is colored in yellow. Molecular surface of residues form the conserved groove and involved in conformational change is displayed in green. Panel B: SnoN chain F. Same as Panel A except that blue was used as a color for the backbone of chain F.
Figure 6.
Superposition of SnoN-DHD, Ski-DHD and DACHbox-N.
Panel A: Superposition of open conformation SnoN-DHD (chain D) and Ski-DHD. SnoN- and Ski-DHD are colored in yellow and red, respectively. Representation of Ski-DHD was limited to residues 97 to 192. Panel B: Superposition of tight conformation SnoN-DHD (chain I) and DACHbox-N. SnoN-DHD and DACHbox-N are colored respectively in blue and violet.