This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1yfv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:27, 2 August 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1yfv.png|left|200px]]
 
-
<!--
+
==STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE==
-
The line below this paragraph, containing "STRUCTURE_1yfv", creates the "Structure Box" on the page.
+
<StructureSection load='1yfv' size='340' side='right'caption='[[1yfv]]' 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'>[[1yfv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YFV 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>
-
-->
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yfv OCA], [https://pdbe.org/1yfv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yfv RCSB], [https://www.ebi.ac.uk/pdbsum/1yfv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yfv ProSAT]</span></td></tr>
-
{{STRUCTURE_1yfv| PDB=1yfv | SCENE= }}
+
</table>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif in the secondary structures of biological RNAs. The three-dimensional structure of (rGGCGAGCC)2 was derived using molecular dynamics and energy minimization with NMR-derived restraints for 78 interproton distances (per strand), 18 hydrogen bonds for the six Watson-Crick G x C pairs, and 26 dihedral angles (per strand). The G x A mismatch structures are similar to those observed in a DNA duplex [Li, Y., Zon, G., &amp; Wilson, W. D. (1991) Proc. Natl. Acad. Sci. U.S.A. 80, 26-30] and an RNA hairpin [Heus, H. A., &amp; Pardi, A. (1991) Science 253, 191-193], with hydrogen bonds from guanine 2-amino and N3 to adenine N7 and 6-amino, respectively. The other G 2-amino and A 6-amino protons are within hydrogen-bonding distance of a phosphate oxygen and 2'-oxygen, respectively. Strong interstrand A-A and G-G stacking is observed between the G x A mismatches. This contrasts with the poor stacking observed between the G x A mismatches and closing G x C base pairs. The stems are basically A-form with all bases in the anti conformation and all nonterminal sugars in the C3'-endo conformation. The structure rationalizes previous thermodynamic, circular dichroism, and imino proton NMR results and suggests tandem G x A mismatches in RNA may provide a contact site for tertiary interactions.
-
===STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE===
+
Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics.,SantaLucia J Jr, Turner DH Biochemistry. 1993 Nov 30;32(47):12612-23. PMID:8251479<ref>PMID:8251479</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_8251479}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1yfv" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 8251479 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_8251479}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFV OCA].
+
[[Category: Synthetic construct]]
-
 
+
[[Category: Santalucia Junior J]]
-
==Reference==
+
[[Category: Turner DH]]
-
Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics., SantaLucia J Jr, Turner DH, Biochemistry. 1993 Nov 30;32(47):12612-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8251479 8251479]
+
-
[[Category: Junior, J Santalucia.]]
+
-
[[Category: Turner, D H.]]
+
-
[[Category: 2-d nmr]]
+
-
[[Category: Anti-parallel rna duplex]]
+
-
[[Category: G:a mismatch]]
+
-
[[Category: Ribonucleic acid]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 00:56:55 2008''
+

Current revision

STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE

PDB ID 1yfv

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yfv"
Personal tools