4rcj: Difference between revisions

Latest revision as of 13:23, 1 July 2026

Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA

Structural highlights

4rcj is a 2 chain structure with sequence from Homo sapiens and Synthetic construct. 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:	6MZ
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YTHD1_HUMAN Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability.^[1]

Publication Abstract from PubMed

N6-methyladenosine (m6A) is the most abundant internal modification in RNA and is specifically recognized by YTH domain containing proteins. Recently we reported that YTHDC1 prefers guanosine and disfavors adenosine at the position preceding the m6A nucleotide in RNA and preferentially binds to the GG(m6A)C sequence. Now we systematically characterized the binding affinities of the YTH domains of three other human proteins and yeast YTH domain protein Pho92, and determined the crystal structures of the YTH domains of human YTHDF1 and yeast Pho92 in complex with a 5-mer m6A RNA, respectively. Our binding and structural data revealed that the YTH domain used a conserved aromatic cage to recognize m6A. Nevertheless, none of these YTH domains, except YTHDC1, display sequence selectivity at the position preceding the m6A modification. Structural comparison of these different YTH domains revealed that among those, only YTHDC1 harbours a distinctly selective binding pocket for the nucleotide preceding the m6A nucleotide.

Structural basis for the discriminative recognition of N6-methyladenosine RNA by the human YT521-B homology domain family of proteins.,Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J J Biol Chem. 2015 Aug 28. pii: jbc.M115.680389. PMID:26318451^[2]

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

References

↑ Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014 Jan 2;505(7481):117-20. doi: 10.1038/nature12730. Epub 2013 Nov 27. PMID:24284625 doi:https://dx.doi.org/10.1038/nature12730
↑ Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J. Structural basis for the discriminative recognition of N6-methyladenosine RNA by the human YT521-B homology domain family of proteins. J Biol Chem. 2015 Aug 28. pii: jbc.M115.680389. PMID:26318451 doi:https://dx.doi.org/10.1074/jbc.M115.680389

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OCA

[1] Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014 Jan 2;505(7481):117-20. doi: 10.1038/nature12730. Epub 2013 Nov 27. PMID:24284625 doi:https://dx.doi.org/10.1038/nature12730

[2] Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J. Structural basis for the discriminative recognition of N6-methyladenosine RNA by the human YT521-B homology domain family of proteins. J Biol Chem. 2015 Aug 28. pii: jbc.M115.680389. PMID:26318451 doi:https://dx.doi.org/10.1074/jbc.M115.680389

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='4rcj' size='340' side='right'caption='[[4rcj]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rcj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RCJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RCJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rcj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RCJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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='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>
+<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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rci|4rci]], [[4rcm|4rcm]]</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=4rcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rcj OCA], [https://pdbe.org/4rcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rcj RCSB], [https://www.ebi.ac.uk/pdbsum/4rcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rcj ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YTHDF1, C20orf21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4rcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rcj OCA], [http://pdbe.org/4rcj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rcj RCSB], [http://www.ebi.ac.uk/pdbsum/4rcj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rcj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YTHD1_HUMAN YTHD1_HUMAN]] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability.<ref>PMID:24284625</ref>
+[https://www.uniprot.org/uniprot/YTHD1_HUMAN YTHD1_HUMAN] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability.<ref>PMID:24284625</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Arrowsmith, C H]]
+[[Category: Synthetic construct]]
-[[Category: Bountra, C]]
+[[Category: Arrowsmith CH]]
-[[Category: Edwards, A M]]
+[[Category: Bountra C]]
-[[Category: Min, J]]
+[[Category: Edwards AM]]
-[[Category: Structural genomic]]
+[[Category: Min J]]
-[[Category: Tempel, W]]
+[[Category: Tempel W]]
-[[Category: Xu, C]]
+[[Category: Xu C]]
-[[Category: Rna binding protein-rna complex]]
-[[Category: Sgc]]

4rcj: Difference between revisions

Latest revision as of 13:23, 1 July 2026

Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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