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1idv

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{{STRUCTURE_1idv| PDB=1idv | SCENE= }}
{{STRUCTURE_1idv| PDB=1idv | SCENE= }}
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'''NMR structure of HCV ires RNA domain IIIC'''
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===NMR structure of HCV ires RNA domain IIIC===
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==Overview==
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Translation of the open reading frames (ORF) of the hepatitis C virus (HCV) and closely related GB virus B (GBV-B) genomes is driven by internal ribosome entry site (IRES) elements located within the 5' non-translated RNA. The functioning of these IRES elements is highly dependent on primary and higher order RNA structures. We present here the solution structures of a common, critical domain within each of these IRESs, stem-loop IIIc. These ten-nucleotide hairpins have nearly identical sequences and similar overall tertiary folds. The final refined structure of each shows a stem with three G:C base-pairs and a novel tetraloop fold. Although the bases are buckled, the first and fourth nucleotides of both tetraloops form a Watson-Crick type base-pair, while the apical nucleotides are located in the major groove where they adopt C(2)-endo sugar puckering with B-form geometry. No hydrogen bonding interactions were observed involving the two apical residues of the tetraloop. Stability of the loops appears to be derived primarily from the stacking of bases, and the hydrogen bonding between the fourth and seventh residues. Mutational analysis shows that the primary sequence of stem-loop IIIc is important for IRES function and that the stem and first and fourth nucleotides of the tetraloop contribute to the efficiency of internal ribosome entry. Base-pair formation between these two positions is essential. In contrast, the apical loop nucleotides differ between HCV and GBV-B, and substitutions in this region of the hairpin are tolerated without major loss of function.
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{{ABSTRACT_PUBMED_15476802}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IDV OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IDV OCA].
==Reference==
==Reference==
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[[Category: Ire]]
[[Category: Ire]]
[[Category: Stem-loop]]
[[Category: Stem-loop]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 10:49:10 2008''

Revision as of 07:49, 1 July 2008

Image:1idv.png

Template:STRUCTURE 1idv

NMR structure of HCV ires RNA domain IIIC

Template:ABSTRACT PUBMED 15476802

About this Structure

Full experimental information is available from OCA.

Reference

Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites., Rijnbrand R, Thiviyanathan V, Kaluarachchi K, Lemon SM, Gorenstein DG, J Mol Biol. 2004 Oct 29;343(4):805-17. PMID:15476802

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