3hvr: Difference between revisions

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{{Seed}}
[[Image:3hvr.jpg|left|200px]]


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==Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site==
The line below this paragraph, containing "STRUCTURE_3hvr", creates the "Structure Box" on the page.
<StructureSection load='3hvr' size='340' side='right'caption='[[3hvr]], [[Resolution|resolution]] 3.21&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'>[[3hvr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HVR 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]] 3.211&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
{{STRUCTURE_3hvr|  PDB=3hvr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hvr OCA], [https://pdbe.org/3hvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hvr RCSB], [https://www.ebi.ac.uk/pdbsum/3hvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hvr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q746M7_THET2 Q746M7_THET2]
== 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/hv/3hvr_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=3hvr ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here we report on structures of ternary complexes of Thermus thermophilus Ago catalytic mutants with 5'-phosphorylated 21-nucleotide guide DNA and complementary target RNAs of 12, 15 and 19 nucleotides in length, which define the molecular basis for Mg(2+)-facilitated site-specific cleavage of the target. We observe pivot-like domain movements within the Ago scaffold on proceeding from nucleation to propagation steps of guide-target duplex formation, with duplex zippering beyond one turn of the helix requiring the release of the 3'-end of the guide from the PAZ pocket. Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures.


===Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site===
Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes.,Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ Nature. 2009 Oct 8;461(7265):754-61. PMID:19812667<ref>PMID:19812667</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3hvr" style="background-color:#fffaf0;"></div>


==About this Structure==
==See Also==
3HVR is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HVR OCA].
*[[Argonaute 3D structures|Argonaute 3D structures]]
[[Category: Thermus thermophilus hb27]]
== References ==
[[Category: Li, H.]]
<references/>
[[Category: Patel, D J.]]
__TOC__
[[Category: Sheng, G.]]
</StructureSection>
[[Category: Wang, Y.]]
[[Category: Large Structures]]
[[Category: Argonaute]]
[[Category: Thermus thermophilus HB27]]
[[Category: Nucleic acid binding protein/dna/rna complex]]
[[Category: Li H]]
[[Category: Plasmid]]
[[Category: Patel DJ]]
[[Category: Protein-dna-rna complex]]
[[Category: Sheng G]]
 
[[Category: Wang Y]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct  7 14:12:05 2009''
Retrieved from "https://proteopedia.org/3hvr"