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.


3d3j

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:03, 1 November 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3d3j.png|left|200px]]
 
-
<!--
+
==Crystal structure of human Edc3p==
-
The line below this paragraph, containing "STRUCTURE_3d3j", creates the "Structure Box" on the page.
+
<StructureSection load='3d3j' size='340' side='right'caption='[[3d3j]], [[Resolution|resolution]] 2.80&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'>[[3d3j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D3J 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]] 2.8&#8491;</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=3d3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d3j OCA], [https://pdbe.org/3d3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d3j RCSB], [https://www.ebi.ac.uk/pdbsum/3d3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d3j ProSAT]</span></td></tr>
-
{{STRUCTURE_3d3j| PDB=3d3j | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/EDC3_HUMAN EDC3_HUMAN] Binds single-stranded RNA. In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in spermiogenesis and oogenesis.<ref>PMID:16364915</ref> <ref>PMID:17533573</ref> <ref>PMID:18678652</ref>
 +
== 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/d3/3d3j_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=3d3j ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Edc3 is an enhancer of decapping and serves as a scaffold that aggregates mRNA ribonucleoproteins together for P-body formation. Edc3 forms a network of interactions with the components of the mRNA decapping machinery and has a modular domain architecture consisting of an N-terminal Lsm domain, a central FDF domain, and a C-terminal YjeF-N domain. We have determined the crystal structure of the N-terminally truncated human Edc3 at a resolution of 2.2 A. The structure reveals that the YjeF-N domain of Edc3 possesses a divergent Rossmann fold topology that forms a dimer, which is supported by sedimentation velocity and sedimentation equilibrium analysis in solution. The dimerization interface of Edc3 is highly conserved in eukaryotes despite the overall low sequence homology across species. Structure-based site-directed mutagenesis revealed dimerization is required for efficient RNA binding, P-body formation, and likely for regulating the yeast Rps28B mRNA as well, suggesting that the dimeric form of Edc3 is a structural and functional unit in mRNA degradation.
-
===Crystal structure of human Edc3p===
+
Crystal structure of human Edc3 and its functional implications.,Ling SH, Decker CJ, Walsh MA, She M, Parker R, Song H Mol Cell Biol. 2008 Oct;28(19):5965-76. Epub 2008 Aug 4. PMID:18678652<ref>PMID:18678652</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_18678652}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3d3j" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 18678652 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18678652}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
3D3J is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D3J OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:18678652</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Ling, S H.M.]]
+
[[Category: Large Structures]]
-
[[Category: Cytoplasm]]
+
[[Category: Ling SHM]]
-
[[Category: Hedc3]]
+
-
[[Category: Phosphoprotein]]
+
-
[[Category: Protein binding]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:49:59 2009''
+

Current revision

Crystal structure of human Edc3p

PDB ID 3d3j

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/3d3j"
Personal tools