1rfr: Difference between revisions

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


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==NMR structure of the 30mer stemloop-D of coxsackieviral RNA==
The line below this paragraph, containing "STRUCTURE_1rfr", creates the "Structure Box" on the page.
<StructureSection load='1rfr' size='340' side='right'caption='[[1rfr]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1rfr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_B3 Coxsackievirus B3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RFR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rfr OCA], [https://pdbe.org/1rfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rfr RCSB], [https://www.ebi.ac.uk/pdbsum/1rfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rfr ProSAT]</span></td></tr>
{{STRUCTURE_1rfr|  PDB=1rfr  |  SCENE=  }}
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===NMR structure of the 30mer stemloop-D of coxsackieviral RNA===
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<ref>PMID:14962384</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_14962384}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1rfr" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 14962384 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_14962384}}
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</StructureSection>
==About this Structure==
[[Category: Coxsackievirus B3]]
1RFR is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Human_coxsackievirus_b3 Human coxsackievirus b3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RFR OCA].
[[Category: Large Structures]]
 
[[Category: Bucci E]]
==Reference==
[[Category: Gorlach M]]
<ref group="xtra">PMID:14962384</ref><references group="xtra"/>
[[Category: Hafner S]]
[[Category: Human coxsackievirus b3]]
[[Category: Ohlenschlager O]]
[[Category: Bucci, E.]]
[[Category: Ramachandran R]]
[[Category: Gorlach, M.]]
[[Category: Seitz S]]
[[Category: Hafner, S.]]
[[Category: Wohnert J]]
[[Category: Ohlenschlager, O.]]
[[Category: Zell R]]
[[Category: Ramachandran, R.]]
[[Category: Seitz, S.]]
[[Category: Wohnert, J.]]
[[Category: Zell, R.]]
[[Category: A-form helix stem]]
[[Category: Base-paired u:u-c:u-u:u mismatch]]
[[Category: Loop with conformation similar to stable uncg-tetraloops and u:g closing base pair]]
[[Category: Rna]]
 
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