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3omc

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Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s

Structural highlights

3omc is a 4 chain structure with sequence from Homo sapiens and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.77Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SND1_HUMAN Functions as a bridging factor between STAT6 and the basal transcription factor. Plays a role in PIM1 regulation of MYB activity. Functions as a transcriptional coactivator for the Epstein-Barr virus nuclear antigen 2 (EBNA2).^[1]

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

Arginine methylation modulates diverse cellular processes and represents a molecular signature of germ-line-specific Piwi family proteins. A subset of Tudor domains recognize arginine methylation modifications, but the binding mechanism has been lacking. Here we establish that, like other germ-line Tudor proteins, the ancestral staphylococcal nuclease domain-containing 1 (SND1) polypeptide is expressed and associates with PIWIL1/Miwi in germ cells. We find that human SND1 binds PIWIL1 in an arginine methylation-dependent manner with a preference for symmetrically dimethylated arginine. The entire Tudor domain and a bifurcated SN domain are required for this binding activity, whereas the canonical Tudor domain alone is insufficient for methylarginine ligand binding. Crystal structures show that the intact SND1 extended Tudor domain forms a wide and negatively charged binding groove, which can accommodate distinct symmetrically dimethylated arginine peptides from PIWIL1 in different orientations. This analysis explains how SND1 preferentially recognizes symmetrical dimethylarginine via an aromatic cage and conserved hydrogen bonds, and provides a general paradigm for the binding mechanisms of methylarginine-containing peptides by extended Tudor domains.

Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain.,Liu K, Chen C, Guo Y, Lam R, Bian C, Xu C, Zhao DY, Jin J, MacKenzie F, Pawson T, Min J Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18398-403. Epub 2010 Oct 11. PMID:20937909^[2]

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

References

↑ Tong X, Drapkin R, Yalamanchili R, Mosialos G, Kieff E. The Epstein-Barr virus nuclear protein 2 acidic domain forms a complex with a novel cellular coactivator that can interact with TFIIE. Mol Cell Biol. 1995 Sep;15(9):4735-44. PMID:7651391
↑ Liu K, Chen C, Guo Y, Lam R, Bian C, Xu C, Zhao DY, Jin J, MacKenzie F, Pawson T, Min J. Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain. Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18398-403. Epub 2010 Oct 11. PMID:20937909 doi:10.1073/pnas.1013106107

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/3omc"

@@ Line 1: / Line 1: @@
 ==Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s==
-<StructureSection load='3omc' size='340' side='right' caption='[[3omc]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
+<StructureSection load='3omc' size='340' side='right'caption='[[3omc]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3omc]] 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=3OMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OMC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3omc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OMC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.77&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SND1, TDRD11 ([http://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'>[https://proteopedia.org/fgij/fg.htm?mol=3omc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3omc OCA], [https://pdbe.org/3omc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3omc RCSB], [https://www.ebi.ac.uk/pdbsum/3omc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3omc ProSAT]</span></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=3omc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3omc OCA], [http://pdbe.org/3omc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3omc RCSB], [http://www.ebi.ac.uk/pdbsum/3omc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3omc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SND1_HUMAN SND1_HUMAN]] Functions as a bridging factor between STAT6 and the basal transcription factor. Plays a role in PIM1 regulation of MYB activity. Functions as a transcriptional coactivator for the Epstein-Barr virus nuclear antigen 2 (EBNA2).<ref>PMID:7651391</ref>
+[https://www.uniprot.org/uniprot/SND1_HUMAN SND1_HUMAN] Functions as a bridging factor between STAT6 and the basal transcription factor. Plays a role in PIM1 regulation of MYB activity. Functions as a transcriptional coactivator for the Epstein-Barr virus nuclear antigen 2 (EBNA2).<ref>PMID:7651391</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/om/3omc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/om/3omc_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H]]
+[[Category: Large Structures]]
-[[Category: Bian, C B]]
+[[Category: Synthetic construct]]
-[[Category: Bochkarev, A]]
+[[Category: Arrowsmith CH]]
-[[Category: Bountra, C]]
+[[Category: Bian CB]]
-[[Category: Edwards, A M]]
+[[Category: Bochkarev A]]
-[[Category: Guo, Y H]]
+[[Category: Bountra C]]
-[[Category: Lam, R]]
+[[Category: Edwards AM]]
-[[Category: Liu, K]]
+[[Category: Guo YH]]
-[[Category: MacKenzie, F]]
+[[Category: Lam R]]
-[[Category: Min, J]]
+[[Category: Liu K]]
-[[Category: Structural genomic]]
+[[Category: MacKenzie F]]
-[[Category: Weigelt, J]]
+[[Category: Min J]]
-[[Category: Xu, C]]
+[[Category: Weigelt J]]
-[[Category: P100 extended tudor domain]]
+[[Category: Xu C]]
-[[Category: Piwil1/miwi]]
-[[Category: Sgc]]
-[[Category: Snd1]]
-[[Category: Staphylococcal nuclease domain-containing protein 1]]
-[[Category: Symmetrically dimethylated arginine peptides derived from piwil1]]
-[[Category: Tdrd11]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulator]]

3omc

From Proteopedia

Current revision

Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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