6i1d - Revision history

OCA at 11:44, 24 January 2024

OCA — Wed, 24 Jan 2024 11:44:20 GMT

←Older revision		Revision as of 11:44, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6i1d' size='340' side='right'caption='[[6i1d]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='6i1d' size='340' side='right'caption='[[6i1d]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i1d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I1D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i1d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I1D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.28Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~YSH1, BRR5, YLR277C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=559292 Baker~~'~~s yeast])~~, ~~MPE1, YKL059C, YKL316 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=559292 Baker~~'~~s yeast])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i1d OCA], [~~http~~://pdbe.org/6i1d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i1d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i1d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i1d ProSAT]</span></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=6i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i1d OCA], [https://pdbe.org/6i1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i1d RCSB], [https://www.ebi.ac.uk/pdbsum/6i1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i1d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/YSH1_YEAST YSH1_YEAST]] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Has endonuclease activity.<ref>PMID:15037765</ref> [[http://www.uniprot.org/uniprot/MPE1_YEAST MPE1_YEAST]] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB.	+	[https://www.uniprot.org/uniprot/YSH1_YEAST YSH1_YEAST] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Has endonuclease activity.<ref>PMID:15037765</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boreikaite, V]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Casanal, A]]	+	[[Category: Boreikaite V]]
-	[[Category: Degliesposti, G]]	+	[[Category: Casanal A]]
-	[[Category: Girbig, M]]	+	[[Category: Degliesposti G]]
-	[[Category: Hill~~, C H~~]]	+	[[Category: Girbig M]]
-	[[Category: Kubik, P]]	+	[[Category: Hill CH]]
-	[[Category: Kumar, A]]	+	[[Category: Kubik P]]
-	~~[[Category: Loeffelholz, O von~~]]	+	[[Category: Kumar A]]
-	[[Category: Mariani, A]]	+	[[Category: Mariani A]]
-	[[Category: Maslen, S]]	+	[[Category: Maslen S]]
-	[[Category: Passmore~~, L A~~]]	+	[[Category: Passmore LA]]
-	[[Category: Skehel, M]]	+	[[Category: Skehel M]]
-	[[Category: ~~3' end]]~~	+	[[Category: Von Loeffelholz O]]
-	~~[[Category: Cleavage]]~~	+
-	~~[[Category: Cpf]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: Metallo-beta-lactamase]]~~	+
-	~~[[Category: Mrna]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Polya]]~~	+
-	~~[[Category: Polyadenylation]]~~	+
-	~~[[Category: Pre-mrna~~]]	+

OCA at 08:18, 3 April 2019

OCA — Wed, 03 Apr 2019 08:18:31 GMT

←Older revision		Revision as of 08:18, 3 April 2019
Line 1:		Line 1:

	==Structure of the Ysh1-Mpe1 nuclease complex from S.cerevisiae==		==Structure of the Ysh1-Mpe1 nuclease complex from S.cerevisiae==
-	<StructureSection load='6i1d' size='340' side='right' caption='[[6i1d]], [[Resolution\|resolution]] 2.28Å' scene=''>	+	<StructureSection load='6i1d' size='340' side='right'caption='[[6i1d]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6i1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I1D FirstGlance]. <br>		<table><tr><td colspan='2'>[[6i1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I1D FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Boreikaite, V]]		[[Category: Boreikaite, V]]
	[[Category: Casanal, A]]		[[Category: Casanal, A]]

OCA at 08:46, 21 February 2019

OCA — Thu, 21 Feb 2019 08:46:01 GMT

←Older revision		Revision as of 08:46, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6i1d' size='340' side='right' caption='[[6i1d]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='6i1d' size='340' side='right' caption='[[6i1d]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I1D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YSH1, BRR5, YLR277C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), MPE1, YKL059C, YKL316 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=6i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i1d OCA], [http://pdbe.org/6i1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i1d RCSB], [http://www.ebi.ac.uk/pdbsum/6i1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i1d 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=6i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i1d OCA], [http://pdbe.org/6i1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i1d RCSB], [http://www.ebi.ac.uk/pdbsum/6i1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i1d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/YSH1_YEAST YSH1_YEAST]] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Has endonuclease activity.<ref>PMID:15037765</ref> [[http://www.uniprot.org/uniprot/MPE1_YEAST MPE1_YEAST]] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB.		[[http://www.uniprot.org/uniprot/YSH1_YEAST YSH1_YEAST]] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Has endonuclease activity.<ref>PMID:15037765</ref> [[http://www.uniprot.org/uniprot/MPE1_YEAST MPE1_YEAST]] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The cleavage reaction defines the 3' end of the mature mRNA, and thus the activity of the endonuclease is highly regulated. Here, we show that reconstitution of specific pre-mRNA cleavage with recombinant yeast proteins requires incorporation of the Ysh1 endonuclease into an eight-subunit "CPFcore" complex. Cleavage also requires the accessory cleavage factors IA and IB, which bind substrate pre-mRNAs and CPF, likely facilitating assembly of an active complex. Using X-ray crystallography, electron microscopy, and mass spectrometry, we determine the structure of Ysh1 bound to Mpe1 and the arrangement of subunits within CPFcore. Together, our data suggest that the active mRNA 3' end processing machinery is a dynamic assembly that is licensed to cleave only when all protein factors come together at the polyadenylation site.
		+
		+	Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex.,Hill CH, Boreikaite V, Kumar A, Casanal A, Kubik P, Degliesposti G, Maslen S, Mariani A, von Loeffelholz O, Girbig M, Skehel M, Passmore LA Mol Cell. 2019 Jan 31. pii: S1097-2765(18)31099-2. doi:, 10.1016/j.molcel.2018.12.023. PMID:30737185<ref>PMID:30737185</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6i1d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Boreikaite, V]]		[[Category: Boreikaite, V]]
	[[Category: Casanal, A]]		[[Category: Casanal, A]]

OCA at 09:31, 13 February 2019

OCA — Wed, 13 Feb 2019 09:31:40 GMT

←Older revision		Revision as of 09:31, 13 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6i1d is ~~ON HOLD~~	+	==Structure of the Ysh1-Mpe1 nuclease complex from S.cerevisiae==
-		+	<StructureSection load='6i1d' size='340' side='right' caption='[[6i1d]], [[Resolution\|resolution]] 2.28Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6i1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I1D FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6i1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i1d OCA], [http://pdbe.org/6i1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i1d RCSB], [http://www.ebi.ac.uk/pdbsum/6i1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i1d ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YSH1_YEAST YSH1_YEAST]] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Has endonuclease activity.<ref>PMID:15037765</ref> [[http://www.uniprot.org/uniprot/MPE1_YEAST MPE1_YEAST]] Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB.
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Boreikaite, V]]
		+	[[Category: Casanal, A]]
		+	[[Category: Degliesposti, G]]
		+	[[Category: Girbig, M]]
		+	[[Category: Hill, C H]]
		+	[[Category: Kubik, P]]
		+	[[Category: Kumar, A]]
		+	[[Category: Loeffelholz, O von]]
		+	[[Category: Mariani, A]]
		+	[[Category: Maslen, S]]
		+	[[Category: Passmore, L A]]
		+	[[Category: Skehel, M]]
		+	[[Category: 3' end]]
		+	[[Category: Cleavage]]
		+	[[Category: Cpf]]
		+	[[Category: Endonuclease]]
		+	[[Category: Gene regulation]]
		+	[[Category: Metallo-beta-lactamase]]
		+	[[Category: Mrna]]
		+	[[Category: Nuclease]]
		+	[[Category: Polya]]
		+	[[Category: Polyadenylation]]
		+	[[Category: Pre-mrna]]

OCA: Protected "6i1d" [edit=sysop:move=sysop]

OCA — Wed, 07 Nov 2018 10:36:04 GMT

Protected "6i1d" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:36, 7 November 2018

OCA: New page: '''Unreleased structure''' The entry 6i1d is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Nov 2018 10:36:02 GMT

New page: '''Unreleased structure''' The entry 6i1d is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6i1d is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]