1RFR image
Deposition Date 2003-11-10
Release Date 2004-03-23
Last Version Date 2024-05-22
Entry Detail
PDB ID:
1RFR
Keywords:
RNA
Title:
NMR structure of the 30mer stemloop-D of coxsackieviral RNA
Biological Source:
Source Organism:
Human coxsackievirus B3 (Taxon ID: 12072)
Host Organism:
in vitro
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
100
Conformers Submitted:
20
Selection Criteria:
structures with the lowest energy,target function
1RFR validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:stemloop-D RNA of the 5'-cloverleaf of coxsackievirus B3
Chain IDs:A
Chain Length:30
Number of Molecules:1
Biological Source:Human coxsackievirus B3
Ligand Molecules
NA
Primary Citation
The structure of the stemloop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C.
STRUCTURE 12 237 248 (2004)
PMID: 14962384 DOI: 10.1016/S0969-2126(04)00008-5

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
1RFR