1R7W

NMR STRUCTURE OF THE R(GGAGGACAUCCCUCACGGGUGACCGUGGUCCUCC), DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES WITH AUCCCU BULGE

Summary for 1R7W

• Entry DOI: 10.2210/pdb1r7w/pdb
• Related: 1R7Z
• NMR Information: BMRB: 6076
• Descriptor: 34-MER (1 entity in total)
• Functional Keywords: stem-and-loop structure, six-nucleotide bulge, guga tetraloop, rna
• Total number of polymer chains: 1
• Total formula weight: 10897.51

Authors

Du, Z.,Ulyanov, N.B.,Yu, J.,James, T.L. (deposition date: 2003-10-22, release date: 2004-05-25, Last modification date: 2024-05-22)

Primary citation

Du, Z.,Ulyanov, N.B.,Yu, J.,Andino, R.,James, T.L.
NMR Structures of Loop B RNAs from the Stem-Loop IV Domain of the Enterovirus Internal Ribosome Entry Site: A Single C to U Substitution Drastically Changes the Shape and Flexibility of RNA(,).
Biochemistry, 43:5757-5771, 2004

PubMed Abstract: The 5'-untranslated region of positive-strand RNA viruses harbors many cis-acting RNA structural elements that are important for various viral processes such as replication, translation, and packaging of new virions. Among these is loop B RNA of the stem-loop IV domain within the internal ribosomal entry site (IRES) of enteroviruses, including Poliovirus type 1 (PV1). Studies on PV1 have shown that specific recognition of loop B by the first KH (hnRNP K homology) domain of cellular poly(rC)-binding protein 2 (PCBP2) is essential for efficient translation of the viral mRNA. Here we report the NMR solution structures of two representative sequence variants of enteroviral loop B RNA. The two RNA variants differ at only one position (C vs U) within a six-nucleotide asymmetric internal loop sequence that is the binding site for the PCBP2 KH1 domain. Surprisingly, the two RNAs are drastically different in the overall shape and local dynamics of the bulge region. The RNA with the 5'-AUCCCU bulge sequence adopts an overall L shape. Its bulge nucleotides, especially the last four, are highly flexible and not very well defined by NMR. The RNA with the 5'-AUUCCU bulge sequence adopts an overall U shape, and its bulge sequence exhibits only limited flexibility. A detailed analysis of the two RNA structures and their dynamic properties, as well as available sequence data and known KH domain-RNA complex structures, not only provides insights into how loop B RNA might be recognized by the PCBP2 KH1 domain but also suggests a possible correlation between structural flexibility and pre-existing structural features for protein recognition.

PubMed: 15134450
DOI: 10.1021/bi0363228

Experimental method

SOLUTION NMR