3dlr: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 1: Line 1:
[[Image:3dlr.png|left|200px]]
==Crystal structure of the catalytic core domain from PFV integrase==
<StructureSection load='3dlr' size='340' side='right' caption='[[3dlr]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3dlr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DLR FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1cxu|1cxu]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 Human spumaretrovirus])</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dlr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dlr RCSB], [http://www.ebi.ac.uk/pdbsum/3dlr PDBsum]</span></td></tr>
<table>
== 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/dl/3dlr_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Establishment of the stable provirus is an essential step in retroviral replication, orchestrated by integrase (IN), a virus-derived enzyme. Until now, available structural information was limited to the INs of human immunodeficiency virus type 1 (HIV-1), avian sarcoma virus (ASV) and their close orthologs from the Lentivirus and Alpharetrovirus genera. Here, we characterized the in vitro activity of the prototype foamy virus (PFV) IN from the Spumavirus genus and determined the three-dimensional structure of its catalytic core domain (CCD). Recombinant PFV IN displayed robust and almost exclusively concerted integration activity in vitro utilizing donor DNA substrates as short as 16 bp, underscoring its significance as a model for detailed structural studies. Comparison of the HIV-1, ASV and PFV CCD structures highlighted both conserved as well as unique structural features such as organization of the active site and the putative host factor binding face. Despite possessing very limited sequence identity to its HIV counterpart, PFV IN was sensitive to HIV IN strand transfer inhibitors, suggesting that this class of inhibitors target the most conserved features of retroviral IN-DNA complexes.


{{STRUCTURE_3dlr|  PDB=3dlr  |  SCENE=  }}
Functional and structural characterization of the integrase from the prototype foamy virus.,Valkov E, Gupta SS, Hare S, Helander A, Roversi P, McClure M, Cherepanov P Nucleic Acids Res. 2009 Jan;37(1):243-55. Epub 2008 Nov 26. PMID:19036793<ref>PMID:19036793</ref>


===Crystal structure of the catalytic core domain from PFV integrase===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_19036793}}
 
==About this Structure==
[[3dlr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLR OCA].


==See Also==
==See Also==
*[[Retroviral Integrase|Retroviral Integrase]]
*[[Retroviral Integrase|Retroviral Integrase]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:019036793</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Human spumaretrovirus]]
[[Category: Human spumaretrovirus]]
[[Category: Cherepanov, P.]]
[[Category: Cherepanov, P.]]

Revision as of 13:52, 29 September 2014

Crystal structure of the catalytic core domain from PFV integraseCrystal structure of the catalytic core domain from PFV integrase

Structural highlights

3dlr is a 1 chain structure with sequence from Human spumaretrovirus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:1cxu
Gene:pol (Human spumaretrovirus)
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Establishment of the stable provirus is an essential step in retroviral replication, orchestrated by integrase (IN), a virus-derived enzyme. Until now, available structural information was limited to the INs of human immunodeficiency virus type 1 (HIV-1), avian sarcoma virus (ASV) and their close orthologs from the Lentivirus and Alpharetrovirus genera. Here, we characterized the in vitro activity of the prototype foamy virus (PFV) IN from the Spumavirus genus and determined the three-dimensional structure of its catalytic core domain (CCD). Recombinant PFV IN displayed robust and almost exclusively concerted integration activity in vitro utilizing donor DNA substrates as short as 16 bp, underscoring its significance as a model for detailed structural studies. Comparison of the HIV-1, ASV and PFV CCD structures highlighted both conserved as well as unique structural features such as organization of the active site and the putative host factor binding face. Despite possessing very limited sequence identity to its HIV counterpart, PFV IN was sensitive to HIV IN strand transfer inhibitors, suggesting that this class of inhibitors target the most conserved features of retroviral IN-DNA complexes.

Functional and structural characterization of the integrase from the prototype foamy virus.,Valkov E, Gupta SS, Hare S, Helander A, Roversi P, McClure M, Cherepanov P Nucleic Acids Res. 2009 Jan;37(1):243-55. Epub 2008 Nov 26. PMID:19036793[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Valkov E, Gupta SS, Hare S, Helander A, Roversi P, McClure M, Cherepanov P. Functional and structural characterization of the integrase from the prototype foamy virus. Nucleic Acids Res. 2009 Jan;37(1):243-55. Epub 2008 Nov 26. PMID:19036793 doi:10.1093/nar/gkn938

3dlr, resolution 2.20Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3dlr&oldid=2007231"