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.

3d3k

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:52, 2 February 2022

Crystal structure of human Edc3p

Structural highlights

3d3k is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	3d3j
Gene:	EDC3 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3]

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

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 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^[4]

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

References

↑ Fenger-Gron M, Fillman C, Norrild B, Lykke-Andersen J. Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol Cell. 2005 Dec 22;20(6):905-15. PMID:16364915 doi:S1097-2765(05)01726-0
↑ Rudolph C, Sigruener A, Hartmann A, Orso E, Bals-Pratsch M, Gronwald W, Seifert B, Kalbitzer HR, Verdorfer I, Luetjens CM, Ortmann O, Bornstein SR, Schmitz G. ApoA-I-binding protein (AI-BP) and its homologues hYjeF_N2 and hYjeF_N3 comprise the YjeF_N domain protein family in humans with a role in spermiogenesis and oogenesis. Horm Metab Res. 2007 May;39(5):322-35. PMID:17533573 doi:10.1055/s-2007-977699
↑ Ling SH, Decker CJ, Walsh MA, She M, Parker R, Song H. Crystal structure of human Edc3 and its functional implications. Mol Cell Biol. 2008 Oct;28(19):5965-76. Epub 2008 Aug 4. PMID:18678652 doi:10.1128/MCB.00761-08
↑ Ling SH, Decker CJ, Walsh MA, She M, Parker R, Song H. Crystal structure of human Edc3 and its functional implications. Mol Cell Biol. 2008 Oct;28(19):5965-76. Epub 2008 Aug 4. PMID:18678652 doi:10.1128/MCB.00761-08

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/3d3k"

@@ Line 1: / Line 1: @@
 ==Crystal structure of human Edc3p==
-<StructureSection load='3d3k' size='340' side='right' caption='[[3d3k]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='3d3k' size='340' side='right'caption='[[3d3k]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3d3k]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D3K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3d3k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D3K FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3d3j|3d3j]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3d3j|3d3j]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EDC3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EDC3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3d3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d3k OCA], [http://pdbe.org/3d3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d3k RCSB], [http://www.ebi.ac.uk/pdbsum/3d3k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d3k ProSAT]</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=3d3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d3k OCA], [https://pdbe.org/3d3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d3k RCSB], [https://www.ebi.ac.uk/pdbsum/3d3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d3k ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[[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]]
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Ling, S H.M]]
 [[Category: Hedc3]]
 [[Category: Phosphoprotein]]
 [[Category: Protein binding]]

3d3k

From Proteopedia

Revision as of 07:52, 2 February 2022

Crystal structure of human Edc3p

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