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.

2rm4

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Solution Structure of the LSM Domain of Dm EDC3 (Enhancer of DECAPPING 3)

Structural highlights

2rm4 is a 1 chain structure with sequence from Drosophila melanogaster. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EDC3_DROME In the process of mRNA degradation, may play a role in mRNA decapping.

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

Members of the (L)Sm (Sm and Sm-like) protein family are found across all kingdoms of life and play crucial roles in RNA metabolism. The P-body component EDC3 (enhancer of decapping 3) is a divergent member of this family that functions in mRNA decapping. EDC3 is composed of a N-terminal LSm domain, a central FDF domain, and a C-terminal YjeF-N domain. We show that this modular architecture enables EDC3 to interact with multiple components of the decapping machinery, including DCP1, DCP2, and Me31B. The LSm domain mediates DCP1 binding and P-body localization. We determined the three-dimensional structures of the LSm domains of Drosophila melanogaster and human EDC3 and show that the domain adopts a divergent Sm fold that lacks the characteristic N-terminal alpha-helix and has a disrupted beta4-strand. This domain remains monomeric in solution and lacks several features that canonical (L)Sm domains require for binding RNA. The structures also revealed a conserved patch of surface residues that are required for the interaction with DCP1 but not for P-body localization. The conservation of surface and of critical structural residues indicates that LSm domains in EDC3 proteins adopt a similar fold that has separable novel functions that are absent in canonical (L)Sm proteins.

A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting.,Tritschler F, Eulalio A, Truffault V, Hartmann MD, Helms S, Schmidt S, Coles M, Izaurralde E, Weichenrieder O Mol Cell Biol. 2007 Dec;27(24):8600-11. Epub 2007 Oct 8. PMID:17923697^[1]

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

References

↑ Tritschler F, Eulalio A, Truffault V, Hartmann MD, Helms S, Schmidt S, Coles M, Izaurralde E, Weichenrieder O. A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting. Mol Cell Biol. 2007 Dec;27(24):8600-11. Epub 2007 Oct 8. PMID:17923697 doi:10.1128/MCB.01506-07

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2rm4"

Categories: Drosophila melanogaster | Large Structures | Coles M | Tritschler F | Truffault V

@@ Line 1: / Line 1: @@
 ==Solution Structure of the LSM Domain of Dm EDC3 (Enhancer of DECAPPING 3)==
-<StructureSection load='2rm4' size='340' side='right' caption='[[2rm4]], [[NMR_Ensembles_of_Models | 22 NMR models]]' scene=''>
+<StructureSection load='2rm4' size='340' side='right'caption='[[2rm4]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RM4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rm4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RM4 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vc8|2vc8]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2rm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm4 PDBsum]</span></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=2rm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm4 OCA], [https://pdbe.org/2rm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rm4 RCSB], [https://www.ebi.ac.uk/pdbsum/2rm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm4 ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EDC3_DROME EDC3_DROME] In the process of mRNA degradation, may play a role in mRNA decapping.
 == 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/rm/2rm4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rm/2rm4_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].
+</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=2rm4 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2rm4" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 29: / Line 33: @@
 </StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Coles, M.]]
+[[Category: Large Structures]]
-[[Category: Tritschler, F.]]
+[[Category: Coles M]]
-[[Category: Truffault, V.]]
+[[Category: Tritschler F]]
-[[Category: Enhancer of mrna decapping]]
+[[Category: Truffault V]]
-[[Category: P-body component]]
-[[Category: Protein binding]]
-[[Category: Sm-like protein]]

2rm4

From Proteopedia

Current revision

Solution Structure of the LSM Domain of Dm EDC3 (Enhancer of DECAPPING 3)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox