PDBsum entry 2f8k

RNA binding protein/ RNA

PDB id: 2f8k

Contents

Protein chain

84 a.a. *

DNA/RNA

Waters ×117

* Residue conservation analysis

PDB id:

2f8k

Name:

RNA binding protein/ RNA

Title:

Sequence specific recognition of RNA hairpins by the sam domain of vts1

Structure:

5'-r( Up Ap Ap Up Cp Up Up Up Gp Ap Cp Ap Gp Ap Up U)-3'. Chain: b. Engineered: yes. Other_details: sre23. Protein vts1. Chain: a. Synonym: vti1-2 suppressor protein 1. Engineered: yes

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: vts1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.230 R-free: 0.277

Authors:

T.Aviv,Z.Lin,G.Ben-Ari,C.A.Smibert,F.Sicheri

Key ref:

T.Aviv et al. (2006). Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol, 13, 168-176. PubMed id: 16429151 DOI: 10.1038/nsmb1053

Date:

02-Dec-05 Release date: 24-Jan-06

Protein chain

Q08831  (VTS1_YEAST) -  RNA-binding protein VTS1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 523 a.a.

Struc: 84 a.a.

DNA/RNA chain

U-A-A-U-C-U-U-U-G-A-C-A-G-A-U-U 16 bases

DOI no: 10.1038/nsmb1053

Nat Struct Mol Biol 13:168-176 (2006)

PubMed id: 16429151

Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.

T.Aviv, Z.Lin, G.Ben-Ari, C.A.Smibert, F.Sicheri.

ABSTRACT

The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains. Here we report the 2.0-A X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand. Specificity of RNA binding arises from the association of a guanosine loop base with a shallow pocket on the SAM domain and from multiple SAM domain contacts to the unique backbone structure of the loop, defined in part by a nonplanar base pair within the loop. We have validated NNF1 as an endogenous target of Vts1p among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro.

Selected figure(s)

Figure 2.
Figure 2. The SRE pentaloop structure exhibits similarity to the UNCG and SECIS loops. (a) Stereo diagram of the SRE pentaloop. Dashed lines indicate hydrogen bonds. (b,c) Stereo diagrams of the SRE crystal structure overlaid with the UNCG (b, green; PDB entry 1F7Y; ref. 21) and SECIS (c, blue; PDB entry 1WSU; ref. 22) RNA loops, respectively. Superpositions were generated with Swiss-PDB viewer (http://www.expasy.org/spdbv/).

Figure 3.
Figure 3. Features of the Vts1p-SAM–RNA binding interface. (a) Schematic diagram of SRE recognition by Vts1p-SAM. Black dashed lines, hydrogen bonds; green dashed lines, hydrophobic interactions; blue background, the stem of the SRE; pink background, the pentaloop; red circles, phosphate groups; blue ovals, bridging water molecules. The labeled protein residues are colored according to their originating secondary structure elements as shown in the upper left schematic. (b) Stereo diagram of the Vts1p-SAM–SRE binding interface centered on SRE loop position G3. Red spheres, water molecules participating in bridging interactions between protein and RNA; dashed lines, hydrogen bonds involving the G3 base.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 168-176) copyright 2006.

Figures were selected by an automated process.