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. 2005 May 20;121(4):529-539.
doi: 10.1016/j.cell.2005.03.009.

Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity

Adam J Stein  1 , Gabriele Fuchs  1 , Chunmei Fu  1 , Sandra L Wolin  2 , Karin M Reinisch  3
Affiliations

Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity

Adam J Stein et al. Cell. .

Abstract

The Ro 60 kDa autoantigen is a major target of the immune response in patients with systemic lupus erythematosus. In vertebrate cells, Ro binds misfolded small RNAs and likely functions in RNA quality control. In eukaryotes and bacteria, Ro also associates with small RNAs called Y RNAs. We present structures of unliganded Ro and Ro complexed with two RNAs at 1.95 and 2.2 A resolution, respectively. Ro consists of a von Willebrand factor A domain and a doughnut-shaped domain composed of HEAT repeats. In the complex, a fragment of Y RNA binds on the outer surface of the HEAT-repeat ring, and single-stranded RNA binds in the toroid hole. Mutagenesis supports a binding site for misfolded RNAs that encompasses both sites, with a single-stranded end inserted into the toroid cavity. Our experiments suggest that one role of Y RNAs may be to regulate access of other RNAs to Ro.

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Figures

Figure 1
Figure 1. Structures of Ro and the Ro-RNA complex.
A. A molecular surface representation of Ro with bound RNA shown in pink. Ro is an elliptical toroid. A fragment of Y RNA is bound on its outer surface, and a singlestranded RNA oligonucleotide is bound in the central cavity. The Y RNA fragment is oriented such that in the full-length RNA, the 5′ and 3′ termini would be at the top of the figure (labeled), and the remainder of the RNA (see Figure 3C) would project towards the reader. The MIDAS motif, a divalent cation binding site, is shown in light blue. A 90° rotation about a horizontal axis relates views on the right and left. B. Domain structure of Ro, with orientations as in panel A. Ro consists of a toroid of HEAT repeats and a von Willebrand Factor A (vWFA) domain. Ro is colored from blue at the N-terminus to red at the C-terminus. The MIDAS motif in the vWFA domain is marked with a grey sphere. Helices are labeled H1 through H25, and beta strands are labeled S1 through S13. C. Superimposed backbone traces of unliganded Ro and the Ro-RNA complex. The carbon alpha trace of Ro from the ribonucleoprotein complex (pink) is superimposed on that of unliganded Ro (blue). At left, the carbon alpha traces are aligned using residues 144–278, and at right they are aligned using residues 360–537. Loop 136–143, close to the Y RNA binding surface of Ro, becomes ordered upon RNA binding, and loop 168–175, involved in single stranded RNA binding, rearranges. Asterisks mark the positions of residue 278 (blue) and loops 144–278 and 168–175.
Figure 2
Figure 2. Ro surfaces that interact with RNA.
A. A molecular surface representation of the Ro structure. Surfaces that interact with Y RNA are green while those that interact with single stranded RNA are teal. The views are identical to Figures 1A and 1B. B. Ro colored by electrostatic surface potential. Surfaces that bind RNA have a positive potential, and the vWFA domain is mostly acidic. The asterisk marks the MIDAS motif. C. Ro colored by sequence conservation according to the alignment in panel D. Surface areas where sequences are strictly conserved and similar are red and orange, respectively. Surfaces that interact with Y RNA and with single stranded RNA are conserved as are the characteristic MIDAS motif residues. D. Sequence alignment of Ro proteins from X. laevis, humans, T. nigris, C. elegans, C. reinhardtii, D. radiodurans, and the mycobacteriophage Bxz1 gp220 protein. Residues that are identical in at least 6 of the 7 sequences are red, and residues that are similar (L=V=I, F=Y=W=H, S=T, E=D, R=K, N=Q) in at least 6 of the 7 sequences are orange. Residues in X. laevis Ro that interact with Y RNA are green, and those that interact with single stranded RNA are teal. The beginning of the vWFA domain is indicated by a violet arrow, and residues in the MIDAS motif (D-x-S-x-S…T…D) are violet and marked with violet asterisks. Alpha helices and beta strands are indicated by black and grey bars, respectively, and are numbered as in Figure 1B.
Figure 3
Figure 3. The MIDAS Motif
A. View of the MIDAS motif with Ro in an orientation as in Figure 1B, left panel. Ro is colored as in 1B. Residues in the MIDAS motif are indicated. B. A closer view of the MIDAS motif with Ro in a different orientation. The magnesium ion, shown in pink, is coordinated by S378, S380, T445, an acetate ion (Ac) and two water molecules (w). D376 and D469 form hydrogen bonds to one of these water molecules while Y47 at the Ro N-terminus forms a hydrogen bond to the second water molecule.
Figure 4
Figure 4. Ro interactions with Y RNA and single-stranded RNA
A. Secondary structure diagrams for Xenopus laevis Y3 RNA. Two alternate conformers that may form are shown (Green et al., 1998). RNA bases that were critical for Ro binding in biochemical experiments are pink (Green et al., 1998). The Ro binding site is conserved in all known Y RNAs. B. Fragment of Y RNA bound on the outer surface of Ro. The two RNA oligonucleotides annealed to form the Y RNA mimic are shown in pink and teal. The identity of the nucleotides and the numbering system used in the text are indicated. C. Details of the Ro-Y RNA interaction. Helices from the Ro HEAT repeat domain are shown as cylinders and side chains that interact with RNA are indicated. Helix H9 of Ro appears wedged into the Y RNA duplex, and unpaired nucleotides, which would be part of a bulge in full length Y RNA, are arranged on either side of it. H187 (pink) interacts with C8 at the end of the duplex region. D. Summary of Ro interactions with Y RNA. Uracil bases that are iodinated at the C5 position are indicated with asterisks. Hydrogen bonding interactions (<3.5 Å) are shown by solid lines, and possible electrostatic interactions (< 7 Å) are shown with dotted lines. Atoms in the nucleotide bases that are involved in hydrogen bonds with protein are indicated in grey. Conserved and similar residues in Ro are red and orange, as in Figure 2D. Residues involved in # stacking interactions are boxed in yellow, and residues with extensive van der Waals interactions with nucleotide bases are shown in teal. For clarity, interactions with the RNA ribose rings are not indicated. Interactions mediated by a carbonyl O or an amide N from the protein backbone rather than by a side chain are indicated by “CO” or “N”, respectively. E. Difference (Fo-Fc) electron density for single stranded RNA bound in the central cavity of Ro. The density, from a 2.2 Å map, is shown at three times the r.m.s. variation of the map. The refined model for this portion of RNA is shown in stick presentation. F. Structure of the single stranded RNA bound in the cavity of Ro. Bases U6-A10 (pink) are ordered in both Ro/RNA complexes in the asymmetric unit while G4 and G5 (light pink) are ordered only in one complex. G. Ro interactions with single stranded RNA bound in the central cavity. The notations are as in panel D. Only interactions that are the same in both Ro/RNA complexes in the asymmetric unit are shown.
Figure 5
Figure 5. Binding of wild-type and mutant Ro proteins to Y RNA and misfolded pre-5S rRNA.
A. Effect of shortening the 3’ end of pre-5S rRNA on Ro binding. 32P-labeled misfolded X. laevis oocyte pre-5S rRNA (left) or pre-5S rRNA lacking 8 nt of the 3′ trailer (right) was incubated without protein (lane 1) or with the indicated concentrations of Ro protein (lanes 2–9). The misfolded pre-5S rRNA contains several mutations that cause it to fold efficiently into the structure recognized by Ro (Shi et al., 1996). Protein-RNA complexes were separated from unbound RNA by native gel electrophoresis. B. Binding of mutant Ro proteins to RNA. 32P-labeled Xenopus Y3 RNA (left panels) or misfolded pre-5S rRNA (right panels) was incubated either without protein (lane 1) or with increasing amounts of wild-type Ro (top row) or the indicated mutant proteins (bottom four rows). Protein concentrations are given in nM above lanes 2–9. Protein-RNA complexes were separated from unbound RNA in native gels.
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Comment in

  • Ro's role in RNA reconnaissance.
    MacRae IJ, Doudna JA. MacRae IJ, et al. Cell. 2005 May 20;121(4):495-496. doi: 10.1016/j.cell.2005.05.004. Cell. 2005. PMID: 15907458 Review.

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