1auh: Difference between revisions

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 {{Theoretical_model}}
-{{Seed}}
-[[Image:1auh.png|left|200px]]
-<!--
+==THEORETICAL MODEL OF THE REV BINDING ELEMENT (RBE, 30 RIBONUCLEOTIDE FRAGMENT) OF HUMAN IMMUNODEFICIENCY VIRUS-1 COMPLEXED WITH THE REV PEPTIDE==
-The line below this paragraph, containing "STRUCTURE_1auh", creates the "Structure Box" on the page.
+<StructureSection load='1auh' size='340' side='right'caption='[[1auh]]' 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'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AUH FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=1auh FirstGlance], [https://www.ebi.ac.uk/pdbsum/1auh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1auh ProSAT]</span></td></tr>
--->
+</table>
-{{STRUCTURE_1auh|  PDB=1auh  |  SCENE=  }}
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: In spite of the great interest in the interaction between RNAs and proteins, no general protocol for modelling these complexes is presently available. This methodological vacuum is particularly acute because the structure of few such complexes is known. RESULTS: A general strategy for docking and modelling RNA-protein complexes has been developed. The docking procedure involves minimizing electrostatic and van der Waals' interaction energies of conformationally rigid structures during docking. After docking, libraries of amino acid sidechain conformations are searched to obtain the best interactions between the peptide and the RNA. Using this method, we have reproduced the structure of a bovine immunodeficiency virus (BIV) Tat peptide bound to BIV TAR RNA and have developed a model for the structure of the arginine-rich HIV-1 Rev peptide (Rev34-50) interacting with the Rev-binding element (RBE). CONCLUSIONS: The resulting model of the Rev34-50-RBE complex predicts that although no single arginine sidechain is responsible for complex formation, residues Arg2, Arg5 and Arg11 are more important for binding than the other arginine residues in the peptide. One model is supported by binding measurements performed on wild-type and mutant RBE molecules with the peptide.
-===THEORETICAL MODEL OF THE REV BINDING ELEMENT (RBE, 30 RIBONUCLEOTIDE FRAGMENT) OF HUMAN IMMUNODEFICIENCY VIRUS-1 COMPLEXED WITH THE REV PEPTIDE===
+A docking and modelling strategy for peptide-RNA complexes: applications to BIV Tat-TAR and HIV Rev-RBE.,Srinivasan J, Leclerc F, Xu W, Ellington AD, Cedergren R Fold Des. 1996;1(6):463-72. PMID:9080192<ref>PMID:9080192</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_9080192}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1auh" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 9080192 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9080192}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Theoretical Model]]
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AUH OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:9080192</ref><references group="xtra"/>
 [[Category: Cedergren, R J]]
 [[Category: Ellington, A D]]
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 [[Category: Srinivasan, J]]
 [[Category: Xu, W]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr  8 07:32:27 2010''