3omc

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[[Image:3omc.png|left|200px]]
 
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==Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s==
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The line below this paragraph, containing "STRUCTURE_3omc", creates the "Structure Box" on the page.
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<StructureSection load='3omc' size='340' side='right'caption='[[3omc]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_3omc| PDB=3omc | SCENE= }}
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/om/3omc_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3omc ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s===
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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<ref>PMID:20937909</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_20937909}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3omc" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20937909 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20937909}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[3omc]] is a 4 chain structure with 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=3OMC OCA].
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==Reference==
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<ref group="xtra">PMID:20937909</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Arrowsmith, C H.]]
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[[Category: Large Structures]]
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[[Category: Bian, C B.]]
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[[Category: Synthetic construct]]
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[[Category: Bochkarev, A.]]
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[[Category: Arrowsmith CH]]
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[[Category: Bountra, C.]]
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[[Category: Bian CB]]
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[[Category: Edwards, A M.]]
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[[Category: Bochkarev A]]
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[[Category: Guo, Y H.]]
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[[Category: Bountra C]]
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[[Category: Lam, R.]]
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[[Category: Edwards AM]]
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[[Category: Liu, K.]]
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[[Category: Guo YH]]
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[[Category: MacKenzie, F.]]
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[[Category: Lam R]]
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[[Category: Min, J.]]
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[[Category: Liu K]]
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[[Category: SGC, Structural Genomics Consortium.]]
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[[Category: MacKenzie F]]
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[[Category: Weigelt, J.]]
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[[Category: Min J]]
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[[Category: Xu, C.]]
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[[Category: Weigelt J]]
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[[Category: Xu C]]

Current revision

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

PDB ID 3omc

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OCA

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