PDBsum entry 2es5

RNA

PDB id: 2es5

Contents

DNA/RNA

PDB id:

2es5

Name:

RNA

Title:

Structure of the sre RNA

Structure:

5'-r( Gp Gp Ap Gp Ap Gp Gp Cp Up Cp Up Gp Gp Cp Ap Gp Cp Up Up Up Up Cp C)-3'. Chain: a. Engineered: yes. Other_details: sre RNA

Source:

Synthetic: yes. Other_details: RNA was prepared by in vitro transcription

NMR struc:

20 models

Authors:

F.H.T.Allain

Key ref:

F.C.Oberstrass et al. (2006). Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol, 13, 160-167. PubMed id: 16429156 DOI: 10.1038/nsmb1038

Date:

25-Oct-05 Release date: 24-Jan-06

DNA/RNA chain

G-G-A-G-A-G-G-C-U-C-U-G-G-C-A-G-C-U-U-U-U-C-C 23 bases

DOI no: 10.1038/nsmb1038

Nat Struct Mol Biol 13:160-167 (2006)

PubMed id: 16429156

Shape-specific recognition in the structure of the Vts1p SAM domain with RNA.

F.C.Oberstrass, A.Lee, R.Stefl, M.Janis, G.Chanfreau, F.H.Allain.

ABSTRACT

Although the abundant sterile alpha motif (SAM) domain was originally classified as a protein-protein interaction domain, it has recently been shown that certain SAM domains have the ability to bind RNA, defining a new type of post-transcriptional gene regulator. To further understand the function of SAM-RNA recognition, we determined the solution structures of the SAM domain of the Saccharomyces cerevisiae Vts1p (Vts1p-SAM) and the Smaug response element (SRE) stem-loop RNA as a complex and in isolation. The structures show that Vts1p-SAM recognizes predominantly the shape of the SRE rather than its sequence, with the exception of a G located at the tip of the pentaloop. Using microarray gene profiling, we identified several genes in S. cerevisiae that seem to be regulated by Vts1p and contain one or more copies of the SRE.

Selected figure(s)

Figure 3.
Figure 3. Solution structure of Vts1p-SAM domain bound to SRE RNA and molecular basis of the recognition. (a) Vts1p-SAM–SRE complex. Green, side chains important for recognition; magenta dashed lines, possible hydrogen bonds. (b) Stereo view of the most representative structure showing all the interactions important for recognition, colored as in a. (c) Schematic representation of the intermolecular interactions, colored as in a. (d) Surface representation of the protein in complex. Vts1p-SAM is colored by electrostatic potential (blue, positive; red, negative) and the SRE RNA is shown in stick representation.

Figure 5.
Figure 5. Comparison of the Vts1p-SAM–SRE complex with the structures of other SAM domain–containing proteins. (a) Crystal structure of the RuvA SAM-like domain in complex DNA^45 (PDB entry 1C7Y); red and yellow helices correspond to those in Vts1p-SAM shown in d. (b) Crystal structure of the heterodimer formed by the Yan and Mae SAM domains^17 (1SV0), colored light and dark gray, respectively. (c) Crystal structure of the homodimer formed by the EphB2 SAM domain^18 (1B4F). (d) Overlay of the Vts1p-SAM–SRE complex (blue, red and yellow) and the crystal structure of Smaug (light green; 1OXJ) solved in its free state^7.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 160-167) copyright 2006.

Figures were selected by an automated process.