6r84 - Revision history

OCA at 05:22, 11 April 2020

OCA — Sat, 11 Apr 2020 05:22:11 GMT

←Older revision		Revision as of 05:22, 11 April 2020
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	<SX load='6r84' size='340' side='right' viewer='molstar' caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>		<SX load='6r84' size='340' side='right' viewer='molstar' caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r84]] is a 50 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R84 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R84 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r84]] is a 50 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R84 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6R84 FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPL14A, YKL006W, YKL153 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), VMS1, YDR049W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPL14A, YKL006W, YKL153 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), VMS1, YDR049W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=6r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r84 OCA], [http://pdbe.org/6r84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r84 RCSB], [http://www.ebi.ac.uk/pdbsum/6r84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r84 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=6r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r84 OCA], [http://pdbe.org/6r84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r84 RCSB], [http://www.ebi.ac.uk/pdbsum/6r84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r84 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 00:06, 7 March 2020

OCA — Sat, 07 Mar 2020 00:06:55 GMT

←Older revision		Revision as of 00:06, 7 March 2020
Line 1:		Line 1:

	==Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1)==		==Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1)==
-	<~~StructureSection~~ load='6r84' size='340' side='right'caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>	+	<SX load='6r84' size='340' side='right' viewer='molstar' caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6r84]] is a 50 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R84 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6r84]] is a 50 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R84 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6r84" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6r84" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:41, 10 July 2019

OCA — Wed, 10 Jul 2019 06:41:43 GMT

←Older revision		Revision as of 06:41, 10 July 2019
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	<StructureSection load='6r84' size='340' side='right'caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='6r84' size='340' side='right'caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r84]] is a 50 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R84 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r84]] is a 50 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R84 FirstGlance]. <br>
	</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>		</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>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPL14A, YKL006W, YKL153 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), VMS1, YDR049W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=6r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r84 OCA], [http://pdbe.org/6r84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r84 RCSB], [http://www.ebi.ac.uk/pdbsum/6r84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r84 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=6r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r84 OCA], [http://pdbe.org/6r84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r84 RCSB], [http://www.ebi.ac.uk/pdbsum/6r84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r84 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 06:59, 3 July 2019

OCA — Wed, 03 Jul 2019 06:59:01 GMT

←Older revision		Revision as of 06:59, 3 July 2019
Line 1:		Line 1:

-	==Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with ~~presence of~~ Arb1)==	+	==Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1)==
	<StructureSection load='6r84' size='340' side='right'caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='6r84' size='340' side='right'caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 07:07, 26 June 2019

OCA — Wed, 26 Jun 2019 07:07:55 GMT

←Older revision		Revision as of 07:07, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6r84 is ~~ON HOLD~~	+	==Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with presence of Arb1)==
		+	<StructureSection load='6r84' size='340' side='right'caption='[[6r84]], [[Resolution\|resolution]] 3.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r84]] is a 50 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R84 FirstGlance]. <br>
		+	</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>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</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=6r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r84 OCA], [http://pdbe.org/6r84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r84 RCSB], [http://www.ebi.ac.uk/pdbsum/6r84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r84 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RL25_YEAST RL25_YEAST]] This protein binds to a specific region on the 26S rRNA. [[http://www.uniprot.org/uniprot/RL12A_YEAST RL12A_YEAST]] This protein binds directly to 26S ribosomal RNA.[HAMAP-Rule:MF_00736] [[http://www.uniprot.org/uniprot/VMS1_YEAST VMS1_YEAST]] Involved in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway. Component of an evolutionarily conserved system for ubiquitin-mediated mitochondria-associated protein degradation (MAD), which is necessary to maintain mitochondrial, cellular, and organismal viability.<ref>PMID:21070972</ref> <ref>PMID:21148305</ref> [[http://www.uniprot.org/uniprot/ARB1_YEAST ARB1_YEAST]] Stimulates 40S and 60S ribosome biogenesis.<ref>PMID:16260602</ref> [[http://www.uniprot.org/uniprot/RL40A_YEAST RL40A_YEAST]] Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity). 60S ribosomal protein L40-A: Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel (PubMed:22096102). eL40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2 (PubMed:23169626).<ref>PMID:23169626</ref> <ref>PMID:22096102</ref> [[http://www.uniprot.org/uniprot/RL4A_YEAST RL4A_YEAST]] Participates in the regulation of the accumulation of its own mRNA.<ref>PMID:2065661</ref> [[http://www.uniprot.org/uniprot/RLA0_YEAST RLA0_YEAST]] Ribosomal protein P0 is the functional equivalent of E.coli protein L10. [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL11B_YEAST RL11B_YEAST]] Binds to 5S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[http://www.uniprot.org/uniprot/IF6_YEAST IF6_YEAST]] Binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit to form the 80S initiation complex in the cytoplasm. Is also involved in ribosome biogenesis. Associates with pre-60S subunits in the nucleus and is involved in its nuclear export. Cytoplasmic release of TIF6 from 60S subunits and nuclear relocalization is promoted by the GTPase RIA1/EFL1 and by SDO1. Also required for pre-rRNA processing.<ref>PMID:10085284</ref> <ref>PMID:11779510</ref> <ref>PMID:11238882</ref> <ref>PMID:17353896</ref> <ref>PMID:18256024</ref> <ref>PMID:11101899</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes(1-6). After dissociation of ribosomes, the stalled tRNA-bound peptide remains associated with the 60S subunit and extended by Rqc2 by addition of C-terminal alanyl and threonyl residues (CAT tails)(7-9), whereas Vms1 catalyses cleavage and release of the peptidyl-tRNA before or after addition of CAT tails(10-12). In doing so, Vms1 counteracts CAT-tailing of nuclear-encoded mitochondrial proteins that otherwise drive aggregation and compromise mitochondrial and cellular homeostasis(13). Here we present structural and functional insights into the interaction of Saccharomyces cerevisiae Vms1 with 60S subunits in pre- and post-peptidyl-tRNA cleavage states. Vms1 binds to 60S subunits with its Vms1-like release factor 1 (VLRF1), zinc finger and ankyrin domains. VLRF1 overlaps with the Rqc2 A-tRNA position and interacts with the ribosomal A-site, projecting its catalytic GSQ motif towards the CCA end of the tRNA, its Y285 residue dislodging the tRNA A73 for nucleolytic cleavage. Moreover, in the pre-state, we found the ABCF-type ATPase Arb1 in the ribosomal E-site, which stabilizes the delocalized A73 of the peptidyl-tRNA and stimulates Vms1-dependent tRNA cleavage. Our structural analysis provides mechanistic insights into the interplay of the RQC factors Vms1, Rqc2 and Arb1 and their role in the protection of mitochondria from the aggregation of toxic proteins.

-	~~Authors~~:	+	Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis.,Su T, Izawa T, Thoms M, Yamashita Y, Cheng J, Berninghausen O, Hartl FU, Inada T, Neupert W, Beckmann R Nature. 2019 Jun 12. pii: 10.1038/s41586-019-1307-z. doi:, 10.1038/s41586-019-1307-z. PMID:31189955<ref>PMID:31189955</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6r84" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Beckmann, R]]
		+	[[Category: Berninghausen, O]]
		+	[[Category: Cheng, J]]
		+	[[Category: Inada, T]]
		+	[[Category: Izawa, T]]
		+	[[Category: Neupert, W]]
		+	[[Category: Su, T]]
		+	[[Category: Yamashita, Y]]
		+	[[Category: 60s ribosomal subunit]]
		+	[[Category: Arb1]]
		+	[[Category: Ribosome]]
		+	[[Category: Tif6]]
		+	[[Category: Vms1]]

OCA: Protected "6r84" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2019 05:41:38 GMT

Protected "6r84" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:41, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r84 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Apr 2019 05:41:37 GMT

New page: '''Unreleased structure''' The entry 6r84 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6r84 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]