1rfr | pdb_00001rfr
NMR structure of the 30mer stemloop-D of coxsackieviral RNA
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Overview
Stemloop D (SLD) of the 5' cloverleaf RNA is the cognate ligand of the, coxsackievirus B3 (CVB3) 3C proteinase (3Cpro). Both are indispensable, components of the viral replication initiation complex. SLD is a, structurally autonomous subunit of the 5' cloverleaf. The SLD structure, was solved by NMR spectroscopy to an rms deviation of 0.66 A (all heavy, atoms). SLD contains a novel triple pyrimidine mismatch motif with a, central Watson-Crick type C:U pair. SLD is capped by an apical uCACGg, tetraloop adopting a structure highly similar to stable cUNCGg tetraloops., Binding of CVB3 3Cpro induces changes in NMR spectra for nucleotides, adjacent to the triple pyrimidine mismatch and of the tetraloop implying, them as sites of specific SLD:3Cpro interaction. The binding of 3Cpro to, SLD requires the integrity of those structural elements, strongly, suggesting that 3Cpro recognizes a structural motif instead of a specific, sequence.
About this Structure
1RFR is a Protein complex structure of sequences from Human coxsackievirus b1. Full crystallographic information is available from OCA.
Reference
The structure of the stemloop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C., Ohlenschlager O, Wohnert J, Bucci E, Seitz S, Hafner S, Ramachandran R, Zell R, Gorlach M, Structure. 2004 Feb;12(2):237-48. PMID:14962384
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