3gqx: Difference between revisions

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


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==Pyrococcus Horikoshii NOP5 RNA Binding Domain from a twinned crystal form==
The line below this paragraph, containing "STRUCTURE_3gqx", creates the "Structure Box" on the page.
<StructureSection load='3gqx' size='340' side='right'caption='[[3gqx]], [[Resolution|resolution]] 2.50&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'>[[3gqx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GQX 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]] 2.5&#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=IOD:IODIDE+ION'>IOD</scene></td></tr>
{{STRUCTURE_3gqx|  PDB=3gqx  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gqx OCA], [https://pdbe.org/3gqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gqx RCSB], [https://www.ebi.ac.uk/pdbsum/3gqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gqx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O57810_PYRHO O57810_PYRHO]
== 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/gq/3gqx_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=3gqx ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In archaea and eukarya, box C/D ribonucleoprotein (RNP) complexes are responsible for 2'-O-methylation of tRNAs and rRNAs. The archaeal box C/D small RNP complex requires a small RNA component (sRNA) possessing Watson-Crick complementarity to the target RNA along with three proteins: L7Ae, Nop5p, and fibrillarin. Transfer of a methyl group from S-adenosylmethionine to the target RNA is performed by fibrillarin, which by itself has no affinity for the sRNA-target duplex. Instead, it is targeted to the site of methylation through association with Nop5p, which in turn binds to the L7Ae-sRNA complex. To understand how Nop5p serves as a bridge between the targeting and catalytic functions of the box C/D small RNP complex, we have employed alanine scanning to evaluate the interaction between the Pyrococcus horikoshii Nop5p domain and an L7Ae box C/D RNA complex. From these data, we were able to construct an isolated RNA-binding domain (Nop-RBD) that folds correctly as demonstrated by x-ray crystallography and binds to the L7Ae box C/D RNA complex with near wild type affinity. These data demonstrate that the Nop-RBD is an autonomously folding and functional module important for protein assembly in a number of complexes centered on the L7Ae-kinkturn RNP.


===Pyrococcus Horikoshii NOP5 RNA Binding Domain from a twinned crystal form===
Analysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex.,Hardin JW, Reyes FE, Batey RT J Biol Chem. 2009 May 29;284(22):15317-24. Epub 2009 Mar 31. PMID:19336398<ref>PMID:19336398</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_19336398}}, adds the Publication Abstract to the page
<div class="pdbe-citations 3gqx" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 19336398 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19336398}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3GQX is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GQX OCA].
 
==Reference==
<ref group="xtra">PMID:19336398</ref><references group="xtra"/>
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
[[Category: Batey, R T.]]
[[Category: Batey RT]]
[[Category: Hardin, J W.]]
[[Category: Hardin JW]]
[[Category: Reyes, F E.]]
[[Category: Reyes FE]]
[[Category: Rna binding domain]]
[[Category: Rna binding protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 22 11:22:10 2009''

Latest revision as of 07:10, 6 September 2023

Pyrococcus Horikoshii NOP5 RNA Binding Domain from a twinned crystal form

3gqx, resolution 2.50Å

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