2f8k: Difference between revisions

Latest revision as of 09:22, 30 August 2023

Sequence specific recognition of RNA hairpins by the SAM domain of Vts1

Structural highlights

2f8k is a 2 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 2Å
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.

Publication Abstract from PubMed

The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains. Here we report the 2.0-A X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand. Specificity of RNA binding arises from the association of a guanosine loop base with a shallow pocket on the SAM domain and from multiple SAM domain contacts to the unique backbone structure of the loop, defined in part by a nonplanar base pair within the loop. We have validated NNF1 as an endogenous target of Vts1p among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro.

Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.,Aviv T, Lin Z, Ben-Ari G, Smibert CA, Sicheri F Nat Struct Mol Biol. 2006 Feb;13(2):168-76. Epub 2006 Jan 22. PMID:16429151^[3]

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

References

↑ 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:https://dx.doi.org/10.1074/jbc.M101551200
↑ 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
↑ Aviv T, Lin Z, Ben-Ari G, Smibert CA, Sicheri F. Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol. 2006 Feb;13(2):168-76. Epub 2006 Jan 22. PMID:16429151 doi:10.1038/nsmb1053

Proteopedia Page Contributors and Editors (what is this?)

OCA

[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:https://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

[3] Aviv T, Lin Z, Ben-Ari G, Smibert CA, Sicheri F. Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol. 2006 Feb;13(2):168-76. Epub 2006 Jan 22. PMID:16429151 doi:10.1038/nsmb1053

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='2f8k' size='340' side='right'caption='[[2f8k]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2f8k]] is a 2 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=2F8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F8K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2f8k]] is a 2 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=2F8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F8K FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d3d|2d3d]]</div></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]] 2&#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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8k OCA], [https://pdbe.org/2f8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f8k RCSB], [https://www.ebi.ac.uk/pdbsum/2f8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f8k ProSAT]</span></td></tr>
 </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>
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Aviv, T]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Ben-Ari, G]]
+[[Category: Aviv T]]
-[[Category: Lin, Z]]
+[[Category: Ben-Ari G]]
-[[Category: Sicheri, F]]
+[[Category: Lin Z]]
-[[Category: Smibert, C A]]
+[[Category: Sicheri F]]
-[[Category: Rna binding protein- rna complex]]
+[[Category: Smibert CA]]
-[[Category: Sam domain]]
-[[Category: Vts1-rna complex]]

2f8k: Difference between revisions

Latest revision as of 09:22, 30 August 2023

Sequence specific recognition of RNA hairpins by the SAM domain of Vts1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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