This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1u04

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1u04" size="450" color="white" frame="true" align="right" spinBox="true" caption="1u04, resolution 2.25&Aring;" /> '''Crystal structure of...)
Current revision (08:45, 1 May 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1u04.gif|left|200px]]<br /><applet load="1u04" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1u04, resolution 2.25&Aring;" />
 
-
'''Crystal structure of full length Argonaute from Pyrococcus furiosus'''<br />
 
-
==Overview==
+
==Crystal structure of full length Argonaute from Pyrococcus furiosus==
-
Argonaute proteins and small interfering RNAs (siRNAs) are the known, signature components of the RNA interference effector complex RNA-induced, silencing complex (RISC). However, the identity of "Slicer," the enzyme, that cleaves the messenger RNA (mRNA) as directed by the siRNA, has not, been resolved. Here, we report the crystal structure of the Argonaute, protein from Pyrococcus furiosus at 2.25 angstrom resolution. The, structure reveals a crescent-shaped base made up of the amino-terminal, middle, and PIWI domains. The Piwi Argonaute Zwille (PAZ) domain is held, above the base by a "stalk"-like region. The PIWI domain (named for the, protein piwi) is similar to ribonuclease H, with a conserved active site, aspartate-aspartate-glutamate motif, strongly implicating Argonaute as, "Slicer." The architecture of the molecule and the placement of the PAZ, and PIWI domains define a groove for substrate binding and suggest a, mechanism for siRNA-guided mRNA cleavage.
+
<StructureSection load='1u04' size='340' side='right'caption='[[1u04]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1u04]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. The February 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Small Interfering RNA'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_2 10.2210/rcsb_pdb/mom_2008_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U04 FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u04 OCA], [https://pdbe.org/1u04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u04 RCSB], [https://www.ebi.ac.uk/pdbsum/1u04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u04 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q8U3D2_PYRFU Q8U3D2_PYRFU]
 +
== 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/u0/1u04_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=1u04 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1U04 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1U04 OCA].
+
*[[Argonaute 3D structures|Argonaute 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystal structure of Argonaute and its implications for RISC slicer activity., Song JJ, Smith SK, Hannon GJ, Joshua-Tor L, Science. 2004 Sep 3;305(5689):1434-7. Epub 2004 Jul 29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15284453 15284453]
+
[[Category: Large Structures]]
-
[[Category: Pyrococcus furiosus dsm 3638]]
+
[[Category: Pyrococcus furiosus DSM 3638]]
-
[[Category: Single protein]]
+
[[Category: RCSB PDB Molecule of the Month]]
-
[[Category: Hannon, G.J.]]
+
[[Category: Small Interfering RNA]]
-
[[Category: Joshua-Tor, L.]]
+
[[Category: Hannon GJ]]
-
[[Category: Smith, S.K.]]
+
[[Category: Joshua-Tor L]]
-
[[Category: Song, J.J.]]
+
[[Category: Smith SK]]
-
[[Category: argonaute]]
+
[[Category: Song JJ]]
-
[[Category: paz]]
+
-
[[Category: piwi]]
+
-
[[Category: risc]]
+
-
[[Category: rnai]]
+
-
[[Category: rnase h]]
+
-
[[Category: silencing]]
+
-
[[Category: slicer]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:03:45 2007''
+

Current revision

Crystal structure of full length Argonaute from Pyrococcus furiosus

PDB ID 1u04

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1u04"
Personal tools