2d3d

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[[Image:2d3d.gif|left|200px]]<br /><applet load="2d3d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2d3d, resolution 1.60&Aring;" />
 
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'''crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1'''<br />
 
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==Overview==
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==crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1==
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The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1 has a high affinity towards RNA hairpins containing a CUGGC pentaloop. We present the 1.6 Angstroms X-ray crystal structure of the Vts1 SAM domain in its unliganded state, and the NMR solution structure of this domain in its RNA-bound state. Both structures reveal a canonical five helix SAM domain flanked by additional secondary structural elements at the N and C termini. The two structures are essentially identical, implying that no major structural rearrangements occur upon RNA binding. Amide chemical shift changes map the RNA-binding site to a shallow, basic patch at the junction of helix alpha5 and the loop connecting helices alpha1 and alpha2.
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<StructureSection load='2d3d' size='340' side='right'caption='[[2d3d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3D FirstGlance]. <br>
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2D3D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3D OCA].
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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]] 1.6&#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=CA:CALCIUM+ION'>CA</scene></td></tr>
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==Reference==
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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=2d3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3d OCA], [https://pdbe.org/2d3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3d RCSB], [https://www.ebi.ac.uk/pdbsum/2d3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3d ProSAT]</span></td></tr>
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The NMR and X-ray structures of the Saccharomyces cerevisiae Vts1 SAM domain define a surface for the recognition of RNA hairpins., Aviv T, Amborski AN, Zhao XS, Kwan JJ, Johnson PE, Sicheri F, Donaldson LW, J Mol Biol. 2006 Feb 17;356(2):274-9. Epub 2005 Dec 7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16375924 16375924]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/VTS1_YEAST VTS1_YEAST] RNA-binding protein involved in post-transcriptional regulation through transcript degradation of SRE (SMG-recognition elements) bearing mRNAs. May be involved in vacuolar protein transport.<ref>PMID:11445562</ref> <ref>PMID:12858164</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/d3/2d3d_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2d3d ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Amborski AN]]
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[[Category: Amborski, A N.]]
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[[Category: Aviv T]]
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[[Category: Aviv, T.]]
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[[Category: Donaldson LW]]
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[[Category: Donaldson, L W.]]
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[[Category: Johnson PE]]
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[[Category: Johnson, P E.]]
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[[Category: Kwan JJ]]
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[[Category: Kwan, J J.]]
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[[Category: Sicheri F]]
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[[Category: Sicheri, F.]]
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[[Category: Zhao XS]]
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[[Category: Zhao, X S.]]
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[[Category: CA]]
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[[Category: rna binding]]
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[[Category: sam domain]]
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[[Category: sre hairpin binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:55:01 2008''
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Current revision

crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1

PDB ID 2d3d

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