This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2mtv

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:06, 8 March 2023

Solution Structure of the YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA

Structural highlights

2mtv is a 2 chain structure with sequence from Rattus norvegicus and Synthetic construct. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YTDC1_RAT RNA-binding protein that regulates alternative splice site selection.^[1] ^[2]

Publication Abstract from PubMed

N6A methylation is the most abundant RNA modification occurring within messenger RNA. Impairment of methylase or demethylase functions are associated with severe phenotypes and diseases in several organisms. Beside writer and eraser enzymes of this dynamic RNA epigenetic modification, reader proteins that recognize this modification are involved in numerous cellular processes. Although the precise characterization of these reader proteins remains unknown, preliminary data showed that most potential reader proteins contained a conserved YT521-B homology (YTH) domain. Here we define the YTH domain of rat YT521-B as a N6-methylated adenosine reader domain and report its solution structure in complex with a N6-methylated RNA. The structure reveals a binding preference for NGANNN RNA hexamer and a deep hydrophobic cleft for m6A recognition. These findings establish a molecular function for YTH domains as m6A reader domains and should guide further studies into the biological functions of YTH-containing proteins in m6A recognition.

Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA.,Theler D, Dominguez C, Blatter M, Boudet J, Allain FH Nucleic Acids Res. 2014 Nov 11. pii: gku1116. PMID:25389274^[3]

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

References

↑ Hartmann AM, Nayler O, Schwaiger FW, Obermeier A, Stamm S. The interaction and colocalization of Sam68 with the splicing-associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59(fyn). Mol Biol Cell. 1999 Nov;10(11):3909-26. PMID:10564280
↑ Imai Y, Matsuo N, Ogawa S, Tohyama M, Takagi T. Cloning of a gene, YT521, for a novel RNA splicing-related protein induced by hypoxia/reoxygenation. Brain Res Mol Brain Res. 1998 Jan;53(1-2):33-40. PMID:9473574
↑ Theler D, Dominguez C, Blatter M, Boudet J, Allain FH. Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA. Nucleic Acids Res. 2014 Nov 11. pii: gku1116. PMID:25389274 doi:http://dx.doi.org/10.1093/nar/gku1116

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2mtv"

@@ Line 1: / Line 1: @@
 ==Solution Structure of the YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA==
-<StructureSection load='2mtv' size='340' side='right'caption='[[2mtv]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2mtv' size='340' side='right'caption='[[2mtv]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2mtv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MTV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2mtv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MTV FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ythdc1, Yt521 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=2mtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mtv OCA], [https://pdbe.org/2mtv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mtv RCSB], [https://www.ebi.ac.uk/pdbsum/2mtv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mtv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/YTDC1_RAT YTDC1_RAT]] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:10564280</ref> <ref>PMID:9473574</ref>
+[https://www.uniprot.org/uniprot/YTDC1_RAT YTDC1_RAT] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:10564280</ref> <ref>PMID:9473574</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Buffalo rat]]
 [[Category: Large Structures]]
-[[Category: Allain, F H.T]]
+[[Category: Rattus norvegicus]]
-[[Category: Blatter, M]]
+[[Category: Synthetic construct]]
-[[Category: Boudet, J]]
+[[Category: Allain FH-T]]
-[[Category: Dominguez, C]]
+[[Category: Blatter M]]
-[[Category: Theler, D]]
+[[Category: Boudet J]]
-[[Category: M6a]]
+[[Category: Dominguez C]]
-[[Category: Rna binding protein-rna complex]]
+[[Category: Theler D]]
-[[Category: Yth]]

2mtv

From Proteopedia

Revision as of 08:06, 8 March 2023

Solution Structure of the YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox