2d3d: Difference between revisions

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<StructureSection load='2d3d' size='340' side='right'caption='[[2d3d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='2d3d' size='340' side='right'caption='[[2d3d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2d3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. 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>
<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>
</td></tr><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>
</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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Vts1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
<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>
<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>
</table>
== 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:16375924<ref>PMID:16375924</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2d3d" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 18824]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Amborski, A N]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Aviv, T]]
[[Category: Amborski AN]]
[[Category: Donaldson, L W]]
[[Category: Aviv T]]
[[Category: Johnson, P E]]
[[Category: Donaldson LW]]
[[Category: Kwan, J J]]
[[Category: Johnson PE]]
[[Category: Sicheri, F]]
[[Category: Kwan JJ]]
[[Category: Zhao, X S]]
[[Category: Sicheri F]]
[[Category: Rna binding]]
[[Category: Zhao XS]]
[[Category: Rna binding protein]]
[[Category: Sam domain]]
[[Category: Sre hairpin binding]]

Latest revision as of 16:46, 13 March 2024

crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1crystal structure of the RNA binding SAM domain of saccharomyces cerevisiae Vts1

Structural highlights

2d3d is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Dilcher M, Kohler B, von Mollard GF. Genetic interactions with the yeast Q-SNARE VTI1 reveal novel functions for the R-SNARE YKT6. J Biol Chem. 2001 Sep 14;276(37):34537-44. Epub 2001 Jul 9. PMID:11445562 doi:http://dx.doi.org/10.1074/jbc.M101551200
  2. ↑ Aviv T, Lin Z, Lau S, Rendl LM, Sicheri F, Smibert CA. The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat Struct Biol. 2003 Aug;10(8):614-21. PMID:12858164 doi:10.1038/nsb956

2d3d, resolution 1.60Å

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