6r5k - Revision history

OCA at 05:17, 11 April 2020

OCA — Sat, 11 Apr 2020 05:17:41 GMT

←Older revision		Revision as of 05:17, 11 April 2020
Line 3:		Line 3:
	<SX load='6r5k' size='340' side='right' viewer='molstar' caption='[[6r5k]], [[Resolution\|resolution]] 4.80Å' scene=''>		<SX load='6r5k' size='340' side='right' viewer='molstar' caption='[[6r5k]], [[Resolution\|resolution]] 4.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r5k]] is a 7 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=6R5K OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R5K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r5k]] is a 7 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=6R5K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6R5K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAN2, YGL094C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), PAB1, YER165W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), PAN3, ECM35, YKL025C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAN2, YGL094C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), PAB1, YER165W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), PAN3, ECM35, YKL025C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=6r5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5k OCA], [http://pdbe.org/6r5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r5k RCSB], [http://www.ebi.ac.uk/pdbsum/6r5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5k ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6r5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5k OCA], [http://pdbe.org/6r5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r5k RCSB], [http://www.ebi.ac.uk/pdbsum/6r5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 23:59, 6 March 2020

OCA — Fri, 06 Mar 2020 23:59:28 GMT

←Older revision		Revision as of 23:59, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase==		==Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase==
-	<~~StructureSection~~ load='6r5k' size='340' side='right'caption='[[6r5k]], [[Resolution\|resolution]] 4.80Å' scene=''>	+	<SX load='6r5k' size='340' side='right' viewer='molstar' caption='[[6r5k]], [[Resolution\|resolution]] 4.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6r5k]] is a 7 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=6R5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R5K FirstGlance]. <br>		<table><tr><td colspan='2'>[[6r5k]] is a 7 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=6R5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R5K FirstGlance]. <br>
Line 23:		Line 23:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:24, 12 June 2019

OCA — Wed, 12 Jun 2019 06:24:14 GMT

←Older revision		Revision as of 06:24, 12 June 2019
Line 3:		Line 3:
	<StructureSection load='6r5k' size='340' side='right'caption='[[6r5k]], [[Resolution\|resolution]] 4.80Å' scene=''>		<StructureSection load='6r5k' size='340' side='right'caption='[[6r5k]], [[Resolution\|resolution]] 4.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r5k]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R5K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r5k]] is a 7 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=6R5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R5K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAN2, YGL094C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), PAB1, YER165W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), PAN3, ECM35, YKL025C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=6r5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5k OCA], [http://pdbe.org/6r5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r5k RCSB], [http://www.ebi.ac.uk/pdbsum/6r5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5k 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=6r5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5k OCA], [http://pdbe.org/6r5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r5k RCSB], [http://www.ebi.ac.uk/pdbsum/6r5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5k ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Conti, E]]		[[Category: Conti, E]]

OCA at 06:22, 29 May 2019

OCA — Wed, 29 May 2019 06:22:34 GMT

←Older revision		Revision as of 06:22, 29 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6r5k is ~~ON HOLD~~	+	==Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase==
		+	<StructureSection load='6r5k' size='340' side='right'caption='[[6r5k]], [[Resolution\|resolution]] 4.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r5k]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R5K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=6r5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r5k OCA], [http://pdbe.org/6r5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r5k RCSB], [http://www.ebi.ac.uk/pdbsum/6r5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r5k ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAN3_YEAST PAN3_YEAST]] Regulatory subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA when the poly(A) stretch is bound by poly(A)-binding protein PAB1, which is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping by DCP1-DCP2 and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails, trimming the tails from their synthesized length to the slightly shorter, apparently messenger-specific length found on newly exported mRNAs.. PAN3 acts as a positive regulator for PAN activity, recruiting the catalytic subunit PAN2 to mRNA via its interaction with PAB1. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.<ref>PMID:8816488</ref> <ref>PMID:1358757</ref> <ref>PMID:9774670</ref> <ref>PMID:11953437</ref> <ref>PMID:15894541</ref> [[http://www.uniprot.org/uniprot/PAN2_YEAST PAN2_YEAST]] Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA when the poly(A) stretch is bound by poly(A)-binding protein PAB1, which is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping by DCP1-DCP2 and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails, trimming the tails from their synthesized length to the slightly shorter, apparently messenger-specific length found on newly exported mRNAs. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.<ref>PMID:8550599</ref> <ref>PMID:1358757</ref> <ref>PMID:8816488</ref> <ref>PMID:9774670</ref> <ref>PMID:11239395</ref> <ref>PMID:11953437</ref> <ref>PMID:15630021</ref> <ref>PMID:15894541</ref> [[http://www.uniprot.org/uniprot/PABP_YEAST PABP_YEAST]] Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, interacts with the nuclear cleavage factor IA (CFIA), which is required for both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. Regulates PAN activity via interaction with the stimulator PAN3 or the inhibitor PBP1. In the cytoplasm, affects both translation and mRNA decay. Stimulates translation by interaction with translation initiation factor eIF4G, a subunit of the cap-binding complex eIF4F, bringing the 5'- and 3'-ends of the mRNA in proximity. The formation of this circular mRNP structure appears to be critical for the synergistic effects of the cap and the poly(A) tail in facilitating translation initiation, recycling of ribosomes, and mRNA stability. Also regulates translation termination by recruiting eukaryotic release factor 3 (eRF3). Interaction with eRF3 is also required for regulation of normal mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN. Loss of PAB1 from the mRNP after deadenylation triggers mRNA degradation. Inhibits the major cytoplasmic mRNA deadenylase CCR4-NOT complex. Is also associated peripherally with COPI vesicles through its interaction with ARF1, and this is required for correct localization of the asymmetrically distributed ASH1 mRNA.<ref>PMID:2673535</ref> <ref>PMID:2565532</ref> <ref>PMID:7557393</ref> <ref>PMID:9199303</ref> <ref>PMID:9223284</ref> <ref>PMID:9784497</ref> <ref>PMID:10357826</ref> <ref>PMID:11741542</ref> <ref>PMID:11889048</ref> <ref>PMID:12923185</ref> <ref>PMID:15356266</ref> <ref>PMID:15169912</ref> <ref>PMID:15630021</ref> <ref>PMID:15769879</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The stability of eukaryotic mRNAs is dependent on a ribonucleoprotein (RNP) complex of poly(A)-binding proteins (PABPC1/Pab1) organized on the poly(A) tail. This poly(A) RNP not only protects mRNAs from premature degradation but also stimulates the Pan2-Pan3 deadenylase complex to catalyze the first step of poly(A) tail shortening. We reconstituted this process in vitro using recombinant proteins and show that Pan2-Pan3 associates with and degrades poly(A) RNPs containing two or more Pab1 molecules. The cryo-EM structure of Pan2-Pan3 in complex with a poly(A) RNP composed of 90 adenosines and three Pab1 protomers shows how the oligomerization interfaces of Pab1 are recognized by conserved features of the deadenylase and thread the poly(A) RNA substrate into the nuclease active site. The structure reveals the basis for the periodic repeating architecture at the 3' end of cytoplasmic mRNAs. This illustrates mechanistically how RNA-bound Pab1 oligomers act as rulers for poly(A) tail length over the mRNAs' lifetime.

-	~~Authors~~:	+	Molecular Basis for poly(A) RNP Architecture and Recognition by the Pan2-Pan3 Deadenylase.,Schafer IB, Yamashita M, Schuller JM, Schussler S, Reichelt P, Strauss M, Conti E Cell. 2019 May 14. pii: S0092-8674(19)30399-X. doi: 10.1016/j.cell.2019.04.013. PMID:31104843<ref>PMID:31104843</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6r5k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Conti, E]]
		+	[[Category: Schaefer, I B]]
		+	[[Category: Ccr4-not]]
		+	[[Category: Cryoem]]
		+	[[Category: Deadenylase]]
		+	[[Category: Mrna]]
		+	[[Category: Pab1]]
		+	[[Category: Pabp]]
		+	[[Category: Pan2-pan3]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rnp]]
		+	[[Category: Rrm]]

OCA: Protected "6r5k" [edit=sysop:move=sysop]

OCA — Wed, 03 Apr 2019 04:59:15 GMT

Protected "6r5k" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:59, 3 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r5k is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 03 Apr 2019 04:59:13 GMT

New page: '''Unreleased structure''' The entry 6r5k is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6r5k is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]