RNA recognition and self-association of CPEB4 is mediated by its tandem RRM domains.
Bottom Line: Self-association does not affect the proteins' ability to interact with RNA as demonstrated by ion mobility-mass spectrometry.Chemical shift effects measured by NMR of the apo forms of the RRM1-RRM2 samples indicate that the two domains are orientated toward each other.We propose a model of the CPEB4 RRM1-RRM2-CPE complex that illustrates the experimental data.
Affiliation: Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain.Show MeSH
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Mentions: A comparison of the secondary 13C chemical shifts obtained for the samples to reference values indicate that both RRM1 and RRM2 in the tandem construct adopt the canonical αβ sandwich structure with a β1α1β2β3α2β4 topology with an additional β-strand β4 at the C-terminus of RRM1 (Figure 2A). Comparison of the 13C chemical shifts of RRM1, when assigned independently or in the RRM1–RRM2 construct, indicates that the secondary structure is not altered due to the presence of RRM2 (Figure 2B). For RRM1, a homology model was built using SWISS-MODEL (Template: PDB entry 2DNL, RRM1 of CPEB3, sequence identity 97%, http://swissmodel.expasy.org/; a quality report is shown in Supplementary Figure S1). The topology of the model obtained is consistent with the elements of secondary structure indicated by the analysis of the 13C chemical shifts. The spatial arrangement of the canonical four-stranded antiparallel β-sheet is β4β1β3β2. The homology model we obtained indicates that the additional β4 strand is arranged antiparallel to β4 resulting in the following order for the extended β-sheet: β4’β4β1β3β2.
Affiliation: Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain.