2d3d: Difference between revisions

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-[[Image:2d3d.gif|left|200px]]
- {{Structure
+==crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1==
-|PDB= 2d3d |SIZE=350|CAPTION= <scene name='initialview01'>2d3d</scene>, resolution 1.60&Aring;
+<StructureSection load='2d3d' size='340' side='right'caption='[[2d3d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene>
+<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>
-|ACTIVITY=
+</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>
-|GENE= Vts1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
+<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>
-}}
+<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>
+</table>
-'''crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1'''
+== Function ==
+[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>
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-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.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3d_consurf.spt"</scriptWhenChecked>
-D3D is a [[Single protein]] structure of sequence from [http://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].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-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://www.ncbi.nlm.nih.gov/pubmed/16375924 16375924]
+</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].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Amborski AN]]
-[[Category: Amborski, A N.]]
+[[Category: Aviv T]]
-[[Category: Aviv, T.]]
+[[Category: Donaldson LW]]
-[[Category: Donaldson, L W.]]
+[[Category: Johnson PE]]
-[[Category: Johnson, P E.]]
+[[Category: Kwan JJ]]
-[[Category: Kwan, J J.]]
+[[Category: Sicheri F]]
-[[Category: Sicheri, F.]]
+[[Category: Zhao XS]]
-[[Category: Zhao, X S.]]
-[[Category: CA]]
-[[Category: rna binding]]
-[[Category: sam domain]]
-[[Category: sre hairpin binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:22:49 2008''