1RFR

NMR structure of the 30mer stemloop-D of coxsackieviral RNA

Summary for 1RFR

• Entry DOI: 10.2210/pdb1rfr/pdb
• NMR Information: BMRB: 6042
• Descriptor: stemloop-D RNA of the 5'-cloverleaf of coxsackievirus B3 (1 entity in total)
• Functional Keywords: loop with conformation similar to stable uncg-tetraloops and u:g closing base pair, base-paired u:u-c:u-u:u mismatch, a-form helix stems, rna
• Biological source: Human coxsackievirus B3
• Total number of polymer chains: 1
• Total formula weight: 9536.62

Authors

Ohlenschlager, O.,Wohnert, J.,Bucci, E.,Seitz, S.,Hafner, S.,Ramachandran, R.,Zell, R.,Gorlach, M. (deposition date: 2003-11-10, release date: 2004-03-23, Last modification date: 2024-05-22)

Primary citation

Ohlenschlager, O.,Wohnert, J.,Bucci, E.,Seitz, S.,Hafner, S.,Ramachandran, R.,Zell, R.,Gorlach, M.
The structure of the stemloop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C.
STRUCTURE, 12:237-248, 2004

PubMed Abstract: 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.

PubMed: 14962384
DOI: 10.1016/S0969-2126(04)00008-5

Experimental method

SOLUTION NMR