3hpg: Difference between revisions

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-[[Image:3hpg.png|left|200px]]
-<!--
+==Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces==
-The line below this paragraph, containing "STRUCTURE_3hpg", creates the "Structure Box" on the page.
+<StructureSection load='3hpg' size='340' side='right'caption='[[3hpg]], [[Resolution|resolution]] 3.28&Aring;' 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'>[[3hpg]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Visna/maedi_virus_EV1_KV1772 Visna/maedi virus EV1 KV1772]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HPG 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">X-ray diffraction, [[Resolution|Resolution]] 3.28&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3hpg|  PDB=3hpg  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpg OCA], [https://pdbe.org/3hpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hpg RCSB], [https://www.ebi.ac.uk/pdbsum/3hpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POL_VILVK POL_VILVK] During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hp/3hpg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hpg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Experimental evidence suggests that a tetramer of integrase (IN) is the protagonist of the concerted strand transfer reaction, whereby both ends of retroviral DNA are inserted into a host cell chromosome. Herein we present two crystal structures containing the N-terminal and the catalytic core domains of maedi-visna virus IN in complex with the IN binding domain of the common lentiviral integration co-factor LEDGF. The structures reveal that the dimer-of-dimers architecture of the IN tetramer is stabilized by swapping N-terminal domains between the inner pair of monomers poised to execute catalytic function. Comparison of four independent IN tetramers in our crystal structures elucidate the basis for the closure of the highly flexible dimer-dimer interface, allowing us to model how a pair of active sites become situated for concerted integration. Using a range of complementary approaches, we demonstrate that the dimer-dimer interface is essential for HIV-1 IN tetramerization, concerted integration in vitro, and virus infectivity. Our structures moreover highlight adaptable changes at the interfaces of individual IN dimers that allow divergent lentiviruses to utilize a highly-conserved, common integration co-factor.
-===Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces===
+Structural basis for functional tetramerization of lentiviral integrase.,Hare S, Di Nunzio F, Labeja A, Wang J, Engelman A, Cherepanov P PLoS Pathog. 2009 Jul;5(7):e1000515. Epub 2009 Jul 17. PMID:19609359<ref>PMID:19609359</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_19609359}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3hpg" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19609359 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19609359}}
-==About this Structure==
-[[3hpg]] is a 12 chain structure of [[Retroviral Integrase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Maedi_visna_virus Maedi visna virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPG OCA].
 ==See Also==
-*[[Retroviral Integrase]]
+*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019609359</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Maedi visna virus]]
+[[Category: Large Structures]]
-[[Category: Cherepanov, P.]]
+[[Category: Visna/maedi virus EV1 KV1772]]
-[[Category: Hare, S.]]
+[[Category: Cherepanov P]]
-[[Category: Labeja, A.]]
+[[Category: Hare S]]
-[[Category: Dna integration]]
+[[Category: Labeja A]]
-[[Category: Dna-binding]]
-[[Category: Endonuclease]]
-[[Category: Hhcc motif]]
-[[Category: Host-virus interaction]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Multifunctional enzyme]]
-[[Category: Nuclease]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Nucleus]]
-[[Category: Protein-protein complex]]
-[[Category: Recombination]]
-[[Category: Tetramer]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transferase]]
-[[Category: Viral nucleoprotein]]
-[[Category: Viral protein]]
-[[Category: Virion]]
-[[Category: Zinc]]
-[[Category: Zinc binding]]