U1A RNA-protein complex


Reference: Oubridge, C., Ito, N., Evans, P.R., Teo, C.-H., and Nagai, K. (1994). Crystal structure at 1.92A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 372, 432-438. [Medline abstract]


The U1A signal recognition particle (U1snRNP) is responsible for selection of 5' splice sites in intron splicing. The U1A protein binds to Domain B of the U1snRNA in the U1 snRNP. The U1A protein is a member of the RNP (or RRM) family of proteins, by virtue of the presence of the characteristic RNP motif in the protein sequence. The RNP domain is comprised of the RNP1 and RNP2 motifs. Other members of this family include other snRNP proteins, hnRNP proteins and poly A binding proteins.


To color-code the crystal structure at left, click here < >. The RNP1 motif is shown in green, the RNP2 motif is shown in cyan. Both are beta sheet structures. Other regions of beta sheet are shown in yellow. Helix regions are shown in pink. The same color coding scheme is shown on the protein sequence below. U1A protein sequence

Regions of the RNA which interact with protein are shown in heavy frames on the 3D structure and are boxed in the secondary structure below. Unimportant regions are shown as light, white wireframe. RNA secondary structure

The binding strategy for this interaction is somewhat surprising: the loop residues are splayed out in an extended conformation (in contrast to the anticodon loop of tRNA, for example. In the absence of the protein, the RNA loop appears unstructured, the loop structure seen here is found only in the presence of the protein, which locks it into place by an induced-fit mechanism. Residues in the loop which do not bind protein remain largely unstructured; they vary in conformation depending upon their location in the crystal lattice.

The protein loop between RNP1 and sheet 2 projects through the RNA loop. This region varies in sequence between different members of the RNP family and may account for some of the differences in specificity between different RNP proteins. This loop region plus the RNP1 and RNP2 regions make up the bulk of the contact sites for the RNA. The protein loop is also less structured in the absence of the RNA, so the induced-fit mechanism is mutual for both the RNA and protein.

Hydrogen bonds and stacking interactions

<> A6 of the RNA loop stacks onto the base pairs of the stem. Arg52 of the protein H-bonds to A6 via one of its terminal amines and also to G16 of the stem. The position of arg52 is butressed from behind by H-bonds from the backbone carbonyl group of arg47 to the amide and terminal amines of arg52. Lysine can partially substitute for arg52, but a glutamine substitution is inactive. Red/Blue stereo picture of this view.

<> The exocyclic amine of G9 H-bonds to O2 of U7 and the carbonyl of glu19. The other carbonyl of glu19 H-bonds to U7 as well. The N7 of G9 H-bonds to the terminal amino group of asn15, while the O6 carbonyl of G9 H-bonds to backbone amide N of asn16. The O6 carbonyl also forms a water-mediated H-bond (note the red sphere of the water molecule) to the backbone carbonyl of leu17. N3 of G9 forms 2 other water-mediated H-bonds to the 2'-OH of U7 and to the backbone carbonyl of leu49. Red/Blue stereo picture of this view.

<> O4 of U8 H-bonds to the epsilon amino group of lys80. N3 of U8 H-bonds to the terminal carbonyl of asn16. The sidechain of asn16 is held in place by an H-bond to the amide carbonyl of pro81. O2 of U8 bonds to the terminal amine of arg83 through a water molecule. Red/Blue stereo picture of this view.

<> C10 N4 H-bonds to the amide carbonyl of tyr86 and the terminal carbonyl of gln85, while C10 N3 H-bonds to the amide NH of lys88. C10 also stacks on tyr13 of the RNP2 motif. Changing this tyrosine to a phenylalanine abolishes binding. Note the other direct and water-mediated H-bonds which hold important amino acids in place for binding. Red/Blue stereo picture of this view.

<> C12 stacks upon A11 which is in turn stacked upon phe56. Several peptide backbone H-bonds position C10, A11, and C12 in place. Note the water mediated H-bonds also. Red/Blue stereo picture of this view.

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Comments or Suggestions to:Jim Nolan