6a6j

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Current revision (10:30, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6a6j' size='340' side='right'caption='[[6a6j]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
<StructureSection load='6a6j' size='340' side='right'caption='[[6a6j]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6a6j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A6J FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6a6j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A6J FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.255&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ybx1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6a6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a6j OCA], [https://pdbe.org/6a6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a6j RCSB], [https://www.ebi.ac.uk/pdbsum/6a6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a6j ProSAT]</span></td></tr>
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<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=6a6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a6j OCA], [http://pdbe.org/6a6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a6j RCSB], [http://www.ebi.ac.uk/pdbsum/6a6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a6j ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/YBOX1_HUMAN YBOX1_HUMAN] Mediates pre-mRNA alternative splicing regulation. Binds to splice sites in pre-mRNA and regulates splice site selection. Binds and stabilizes cytoplasmic mRNA. Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Regulates the transcription of numerous genes. Its transcriptional activity on the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes. Promotes separation of DNA strands that contain mismatches or are modified by cisplatin. Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA (in vitro). May play a role in DNA repair. Component of the CRD-mediated complex that promotes MYC mRNA stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in vitro.<ref>PMID:10817758</ref> <ref>PMID:11698476</ref> <ref>PMID:12604611</ref> <ref>PMID:14718551</ref> <ref>PMID:18335541</ref> <ref>PMID:18809583</ref> <ref>PMID:19029303</ref> <ref>PMID:19483673</ref> The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.
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The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the maternal environment is converted to an environment of embryonic-driven development through dramatic reprogramming. However, how maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m(5)C) modification in zebrafish early embryos, we found that m(5)C-modified maternal mRNAs display higher stability than non-m(5)C-modified mRNAs during MZT. We discovered that Y-box binding protein 1 (Ybx1) preferentially recognizes m(5)C-modified mRNAs through pi-pi interactions with a key residue, Trp45, in Ybx1's cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Together with the mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m(5)C-dependent manner. Our study demonstrates an unexpected mechanism of RNA m(5)C-regulated maternal mRNA stabilization during zebrafish MZT, highlighting the critical role of m(5)C mRNA modification in early development.
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RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay.,Yang Y, Wang L, Han X, Yang WL, Zhang M, Ma HL, Sun BF, Li A, Xia J, Chen J, Heng J, Wu B, Chen YS, Xu JW, Yang X, Yao H, Sun J, Lyu C, Wang HL, Huang Y, Sun YP, Zhao YL, Meng A, Ma J, Liu F, Yang YG Mol Cell. 2019 Jul 16. pii: S1097-2765(19)30490-3. doi:, 10.1016/j.molcel.2019.06.033. PMID:31399345<ref>PMID:31399345</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6a6j" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Brachidanio rerio]]
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[[Category: Danio rerio]]
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[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Huang, Y]]
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[[Category: Huang Y]]
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[[Category: Ma, J B]]
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[[Category: Ma JB]]
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[[Category: Wu, B X]]
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[[Category: Wu BX]]
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[[Category: Zhang, M M]]
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[[Category: Zhang MM]]
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[[Category: Ob-fold]]
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[[Category: Rna binding protein-rna complex]]
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Current revision

Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with 6mer m5C RNA

PDB ID 6a6j

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