5ns4

From Proteopedia

Crystal structures of Cy3 cyanine fluorophores stacked onto the end of double-stranded RNA

PDB ID 5ns4

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Structural highlights

5ns4 is a 4 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL5_THETH This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (forming bridge B1b) connecting the head of the 30S subunit to the top of the 50S subunit. The bridge itself contacts the P site tRNA and is implicated in movement during ribosome translocation. Also contacts the P site tRNA independently of the intersubunit bridge; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs (By similarity).[HAMAP-Rule:MF_01333_B]

Publication Abstract from PubMed

The indodicarbocyanine fluorophores Cy3 and Cy5 are extensively used as donor-acceptor pairs in fluorescence resonance energy transfer experiments, especially those involving single molecules. When terminally attached to double-stranded nucleic acids via the 5' phosphate group these fluorophores stack onto the ends of the molecule. Knowledge of the positions of the fluorophores is critical to the interpretation of fluorescence resonance energy transfer data. The positions have been demonstrated for double-stranded (ds) DNA using NMR spectroscopy. Here, we have used x-ray crystallography to analyze the location of Cy3 and Cy5 on dsRNA, using complexes of an RNA stem-loop bound to L5 protein determined at 2.4 A resolution. This confirms the tendency of both fluorophores to stack on the free end of RNA, with the long axis of the fluorophores approximately parallel to that of the terminal basepair. However, the manner of interaction of both Cy3 and Cy5 with the terminus of the dsRNA is significantly different from that deduced for dsDNA using NMR. The fluorophores are stacked on the terminal basepair such that their indole nitrogen atoms lie on the major groove side, and thus their pendant methyl groups are on the minor groove side.

Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA.,Liu Y, Lilley DMJ Biophys J. 2017 Dec 5;113(11):2336-2343. doi: 10.1016/j.bpj.2017.10.002. PMID:29211987^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Liu Y, Lilley DMJ. Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA. Biophys J. 2017 Dec 5;113(11):2336-2343. doi: 10.1016/j.bpj.2017.10.002. PMID:29211987 doi:http://dx.doi.org/10.1016/j.bpj.2017.10.002