2F8K

Sequence specific recognition of RNA hairpins by the SAM domain of Vts1

Summary for 2F8K

• Entry DOI: 10.2210/pdb2f8k/pdb
• Related: 2D3D
• Descriptor: 5'-R(*UP*AP*AP*UP*CP*UP*UP*UP*GP*AP*CP*AP*GP*AP*UP*U)-3', Protein VTS1 (3 entities in total)
• Functional Keywords: vts1-rna complex, sam domain, rna binding protein- rna complex, rna binding protein/ rna
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Cellular location: Cytoplasm: Q08831
• Total number of polymer chains: 2
• Total formula weight: 15124.79

Authors

Aviv, T.,Lin, Z.,Ben-Ari, G.,Smibert, C.A.,Sicheri, F. (deposition date: 2005-12-02, release date: 2006-01-24, Last modification date: 2023-08-30)

Primary citation

Aviv, T.,Lin, Z.,Ben-Ari, G.,Smibert, C.A.,Sicheri, F.
Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.
Nat.Struct.Mol.Biol., 13:168-176, 2006

PubMed 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.

PubMed: 16429151
DOI: 10.1038/nsmb1053

Experimental method

X-RAY DIFFRACTION (2 Å)