1tqr

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[[Image:1tqr.gif|left|200px]]
 
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==NMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to the extremity of the U5 LTR of the HIV-1 genome==
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The line below this paragraph, containing "STRUCTURE_1tqr", creates the "Structure Box" on the page.
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<StructureSection load='1tqr' size='340' side='right'caption='[[1tqr]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1tqr]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TQR FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</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=1tqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tqr OCA], [https://pdbe.org/1tqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tqr RCSB], [https://www.ebi.ac.uk/pdbsum/1tqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tqr ProSAT]</span></td></tr>
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{{STRUCTURE_1tqr| PDB=1tqr | SCENE= }}
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</table>
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<div style="background-color:#fffaf0;">
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'''NMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to the extremity of the U5 LTR of the HIV-1 genome'''
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== Publication Abstract from PubMed ==
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==Overview==
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The integration of the human immunodeficiency virus type 1 DNA into the host cell genome is catalysed by the viral integrase (IN). The reaction consists of a 3'-processing [dinucleotide released from each 3' end of the viral long terminal repeat (LTR)] followed by a strand transfer (insertion of the viral genome into the human chromosome). A 17 base pair oligonucleotide d(GGAAAATCTCTAGCAGT), d(ACTGCTAGAGATTTTCC) reproducing the U5-LTR extremity of viral DNA that contains the IN attachment site was analysed by NMR using the classical NOEs and scalar coupling constants in conjunction with a small set of residual dipolar coupling constants (RDCs) measured at the 13C/15N natural abundance. The combination of these two types of parameters in calculations significantly improved the DNA structure determination. The well-known features of A-tracts were clearly identified by RDCs in the first part of the molecule. The binding/cleavage site at the viral DNA end is distinguishable by a loss of regular base stacking and a distorted minor groove that can aid its specific recognition by IN.
The integration of the human immunodeficiency virus type 1 DNA into the host cell genome is catalysed by the viral integrase (IN). The reaction consists of a 3'-processing [dinucleotide released from each 3' end of the viral long terminal repeat (LTR)] followed by a strand transfer (insertion of the viral genome into the human chromosome). A 17 base pair oligonucleotide d(GGAAAATCTCTAGCAGT), d(ACTGCTAGAGATTTTCC) reproducing the U5-LTR extremity of viral DNA that contains the IN attachment site was analysed by NMR using the classical NOEs and scalar coupling constants in conjunction with a small set of residual dipolar coupling constants (RDCs) measured at the 13C/15N natural abundance. The combination of these two types of parameters in calculations significantly improved the DNA structure determination. The well-known features of A-tracts were clearly identified by RDCs in the first part of the molecule. The binding/cleavage site at the viral DNA end is distinguishable by a loss of regular base stacking and a distorted minor groove that can aid its specific recognition by IN.
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==About this Structure==
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Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase.,Renisio JG, Cosquer S, Cherrak I, El Antri S, Mauffret O, Fermandjian S Nucleic Acids Res. 2005 Apr 6;33(6):1970-81. Print 2005. PMID:15814814<ref>PMID:15814814</ref>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TQR OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase., Renisio JG, Cosquer S, Cherrak I, El Antri S, Mauffret O, Fermandjian S, Nucleic Acids Res. 2005 Apr 6;33(6):1970-81. Print 2005. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15814814 15814814]
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</div>
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[[Category: Antri, S El.]]
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<div class="pdbe-citations 1tqr" style="background-color:#fffaf0;"></div>
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[[Category: Cherrak, I.]]
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== References ==
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[[Category: Cosquer, S.]]
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<references/>
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[[Category: Fermandjian, S.]]
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__TOC__
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[[Category: Mauffret, O.]]
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</StructureSection>
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[[Category: Renisio, J G.]]
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[[Category: Large Structures]]
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[[Category: Double helix]]
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[[Category: Cherrak I]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 10:15:51 2008''
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[[Category: Cosquer S]]
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[[Category: El Antri S]]
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[[Category: Fermandjian S]]
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[[Category: Mauffret O]]
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[[Category: Renisio JG]]

Current revision

NMR Structure of DNA 17-mer GGAAAATCTCTAGCAGT corresponding to the extremity of the U5 LTR of the HIV-1 genome

PDB ID 1tqr

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