User:Wally Novak/Sandbox Whitaker
U5 snRNP
This is a default text for your page Wally Novak/Sandbox Whitaker. Click above on edit this page to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue. FunctionThe U5 snRNA loop 1 interacts directly with the 5’ exon before the first step of splicing and with the 5’ and 3’ exons following the first step of splicing. These U5-exon interactions are essential for tethering and aligning the exons for ligation during the second step of splicing. Structural HighlightsBy deletion analysis of the S. cerevisiae snRNA, we have demonstrated that the minimal U5 snRNA that can complement the lethal phenotype of a U5 gene disruption consists of (i) stem-loop 1, (ii) internal loop 1, (iii) a stem-closing internal loop 1, and (iv) the conserved Sm protein binding site Stem-loop 1: The fungal sequences spanning nt 84 to 110 (S. cerevisiae numbering will be used unless otherwise noted) can be unambiguously aligned with the existing U5 sequences. The central, highly conserved block of 11 nt is flanked, in each case, by two complementary sequences; this region can thus form a stem-loop structure. Internal loop 1: The level of conservation is highest in the 3' half of ILl, where the sequence is invariably CCG in the fungi. In contrast, the fungal and nonfungal sequences that define the 5' halves of ILl are only moderately conserved in comparison to Li and the 3' halves of ILl. Nevertheless, the 5' halves of ILl in all species of U5 include an invariant CG dinucleotide at positions 79 and 80. Sm protein binding site: Putative Sm protein binding sites could be identified in all U5 sequences, thus highlighting the importance of this sequence motif in snRNP assembly (14, 21). The consensus sequence of the fungal U5 Sm sites is R(U)5NGgaa. Protein RoleThe U5 snRNA combines with three other structures to form the U5 snRNP which combines with U4 and U6 to form tri-complex which then becomes incorporated into the spliceosome. 3D StructuresThis is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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