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[[Image:1z30.gif|left|200px]]
{{Seed}}
[[Image:1z30.png|left|200px]]


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{{STRUCTURE_1z30|  PDB=1z30  |  SCENE=  }}  
{{STRUCTURE_1z30|  PDB=1z30  |  SCENE=  }}  


'''NMR structure of the apical part of stemloop D from cloverleaf 1 of bovine enterovirus 1 RNA'''
===NMR structure of the apical part of stemloop D from cloverleaf 1 of bovine enterovirus 1 RNA===




==Overview==
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The 5'-terminal cloverleaf (CL)-like RNA structures are essential for the initiation of positive- and negative-strand RNA synthesis of entero- and rhinoviruses. SLD is the cognate RNA ligand of the viral proteinase 3C (3C(pro)), which is an indispensable component of the viral replication initiation complex. The structure of an 18mer RNA representing the apical stem and the cGUUAg D-loop of SLD from the first 5'-CL of BEV1 was determined in solution to a root-mean-square deviation (r.m.s.d.) (all heavy atoms) of 0.59 A (PDB 1Z30). The first (antiG) and last (synA) nucleotide of the D-loop forms a novel 'pseudo base pair' without direct hydrogen bonds. The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1F7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGUUAg BEV D-loop and the cGUAAg tetraloop differ by 1 nt only. Together with the presented binding data, these findings provide independent experimental evidence for our model [O. Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence.
The line below this paragraph, {{ABSTRACT_PUBMED_15814817}}, adds the Publication Abstract to the page
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{{ABSTRACT_PUBMED_15814817}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z30 OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z30 OCA].  


==Reference==
==Reference==
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[[Category: Cguuag rna tetraloop]]
[[Category: Cguuag rna tetraloop]]
[[Category: Cuncgg-type backbone conformation]]
[[Category: Cuncgg-type backbone conformation]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 17:07:17 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 23:53:37 2008''

Revision as of 20:53, 28 July 2008

File:1z30.png

Template:STRUCTURE 1z30

NMR structure of the apical part of stemloop D from cloverleaf 1 of bovine enterovirus 1 RNA

Template:ABSTRACT PUBMED 15814817

About this Structure

Full experimental information is available from OCA.

Reference

A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA., Ihle Y, Ohlenschlager O, Hafner S, Duchardt E, Zacharias M, Seitz S, Zell R, Ramachandran R, Gorlach M, Nucleic Acids Res. 2005 Apr 6;33(6):2003-11. Print 2005. PMID:15814817

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