5ytv - Revision history

OCA at 08:37, 22 November 2023

OCA — Wed, 22 Nov 2023 08:37:39 GMT

←Older revision		Revision as of 08:37, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5ytv' size='340' side='right'caption='[[5ytv]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5ytv' size='340' side='right'caption='[[5ytv]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ytv]] 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=5YTV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YTV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ytv]] 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=5YTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YTV FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5yts\|5yts]], [[5ytt\|5ytt]], [[5ytx\|5ytx]]</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]] 1.7Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">YBX1, NSEP1, YB1 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5ytv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytv OCA], [https://pdbe.org/5ytv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ytv RCSB], [https://www.ebi.ac.uk/pdbsum/5ytv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytv ProSAT]</span></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=5ytv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytv OCA], [~~http~~://pdbe.org/5ytv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ytv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ytv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytv ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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.	+	[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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Huang, Y~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Yang, X~~]]	+	[[Category: Huang Y]]
-	[[Category: ~~Cauc]]~~	+	[[Category: Yang X]]
-	~~[[Category: Cold-shock domain]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna binding protein-rna complex]]~~	+
-	~~[[Category: Yb1~~]]	+

OCA at 06:23, 19 June 2019

OCA — Wed, 19 Jun 2019 06:23:16 GMT

←Older revision		Revision as of 06:23, 19 June 2019
Line 1:		Line 1:

	==Crystal structure of YB1 cold-shock domain in complex with UCAUCU==		==Crystal structure of YB1 cold-shock domain in complex with UCAUCU==
-	<StructureSection load='5ytv' size='340' side='right' caption='[[5ytv]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5ytv' size='340' side='right'caption='[[5ytv]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ytv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YTV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ytv]] 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=5YTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YTV FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yts\|5yts]], [[5ytt\|5ytt]], [[5ytx\|5ytx]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yts\|5yts]], [[5ytt\|5ytt]], [[5ytx\|5ytx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YBX1, NSEP1, YB1 ([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=5ytv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytv OCA], [http://pdbe.org/5ytv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytv RCSB], [http://www.ebi.ac.uk/pdbsum/5ytv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytv ProSAT]</span></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=5ytv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytv OCA], [http://pdbe.org/5ytv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytv RCSB], [http://www.ebi.ac.uk/pdbsum/5ytv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://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.		[[http://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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA (miRNA) processing; and stress granule assembly. However, the mechanisms in YB-1-mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled RNA-seq (iCLIP-seq) analyses, which defined the RNA-binding consensus sequence of YB-1 as CA(U/C)C. We also reported that through binding to its core motif CAUC in primary transcripts, YB-1 regulates the alternative splicing of a CD44 variable exon and the biogenesis of miR-29b-2 during both Drosha and Dicer steps. To elucidate the molecular basis of the YB-1-RNA interactions, we report high-resolution crystal structures of the YB-1 CSD in complex with different RNA oligos at 1.7 A resolution. The structure revealed that CSD interacts with RNA mainly through pi-pi stacking interactions assembled by four highly conserved aromatic residues. Interestingly, YB-1 CSD forms a homodimer in solution, and we observed that two residues, Tyr-99 and Asp-105, at the dimer interface are important for YB-1 CSD dimerization. Substituting these two residues with Ala reduced CSD's RNA binding activity and abrogated the splicing activation of YB-1 targets. The YB-1 CSD-RNA structures presented here at atomic resolution provide mechanistic insights into gene expression regulated by CSD-containing proteins.
		+
		+	Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA.,Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y J Biol Chem. 2019 Jun 3. pii: RA119.007545. doi: 10.1074/jbc.RA119.007545. PMID:31160337<ref>PMID:31160337</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ytv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Huang, Y]]		[[Category: Huang, Y]]
	[[Category: Yang, X]]		[[Category: Yang, X]]

OCA at 06:28, 5 December 2018

OCA — Wed, 05 Dec 2018 06:28:44 GMT

←Older revision		Revision as of 06:28, 5 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ytv is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of YB1 cold-shock domain in complex with UCAUCU==
-		+	<StructureSection load='5ytv' size='340' side='right' caption='[[5ytv]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~: ~~Yang~~, X., ~~Huang~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ytv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YTV FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~YB1 cold~~-~~shock domain~~ in complex ~~with UCAUCU~~	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yts\|5yts]], [[5ytt\|5ytt]], [[5ytx\|5ytx]]</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5ytv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytv OCA], [http://pdbe.org/5ytv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ytv RCSB], [http://www.ebi.ac.uk/pdbsum/5ytv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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.
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Huang, Y]]
	[[Category: Yang, X]]		[[Category: Yang, X]]
-	[[Category: ~~Huang, Y~~]]	+	[[Category: Cauc]]
		+	[[Category: Cold-shock domain]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rna binding protein-rna complex]]
		+	[[Category: Yb1]]

OCA at 07:10, 27 December 2017

OCA — Wed, 27 Dec 2017 07:10:47 GMT

←Older revision		Revision as of 07:10, 27 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ytv is ON HOLD	+	The entry 5ytv is ON HOLD until Paper Publication

	Authors: Yang, X., Huang, Y.		Authors: Yang, X., Huang, Y.

OCA: Protected "5ytv" [edit=sysop:move=sysop]

OCA — Wed, 29 Nov 2017 04:58:07 GMT

Protected "5ytv" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:58, 29 November 2017

OCA: New page: '''Unreleased structure''' The entry 5ytv is ON HOLD Authors: Yang, X., Huang, Y. Description: Crystal structure of YB1 cold-shock domain in complex with UCAUCU [[Category: Unreleased ...

OCA — Wed, 29 Nov 2017 04:58:06 GMT

New page: '''Unreleased structure''' The entry 5ytv is ON HOLD Authors: Yang, X., Huang, Y. Description: Crystal structure of YB1 cold-shock domain in complex with UCAUCU [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 5ytv is ON HOLD

Authors: Yang, X., Huang, Y.

Description: Crystal structure of YB1 cold-shock domain in complex with UCAUCU
[[Category: Unreleased Structures]]
[[Category: Yang, X]]
[[Category: Huang, Y]]