6sgc - Revision history

OCA at 11:09, 30 March 2022

OCA — Wed, 30 Mar 2022 11:09:34 GMT

←Older revision		Revision as of 11:09, 30 March 2022
Line 3:		Line 3:
	<SX load='6sgc' size='340' side='right' viewer='molstar' caption='[[6sgc]], [[Resolution\|resolution]] 2.80Å' scene=''>		<SX load='6sgc' size='340' side='right' viewer='molstar' caption='[[6sgc]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6sgc]] is a 86 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/European_rabbit European rabbit] and [~~http~~://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6SGC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6sgc]] is a 86 chain structure with sequence from [https://en.wikipedia.org/wiki/European_rabbit European rabbit] and [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SGC FirstGlance]. <br>
	</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>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene>, <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=12A:2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5-MONOPHOSPHATE'>12A</scene>, <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=70U:5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5-MONOPHOSPHATE'>70U</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=12A:2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5-MONOPHOSPHATE'>12A</scene>, <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=70U:5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5-MONOPHOSPHATE'>70U</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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=6sgc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sgc OCA], [~~http~~://pdbe.org/6sgc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6sgc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6sgc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6sgc 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=6sgc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sgc OCA], [https://pdbe.org/6sgc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sgc RCSB], [https://www.ebi.ac.uk/pdbsum/6sgc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sgc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[~~http~~://www.uniprot.org/uniprot/G1SS70_RABIT G1SS70_RABIT]] May play a role during erythropoiesis through regulation of transcription factor DDIT3.[HAMAP-Rule:MF_03122]	+	[[https://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[https://www.uniprot.org/uniprot/G1SS70_RABIT G1SS70_RABIT]] May play a role during erythropoiesis through regulation of transcription factor DDIT3.[HAMAP-Rule:MF_03122]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:09, 11 April 2020

OCA — Sat, 11 Apr 2020 06:09:15 GMT

←Older revision		Revision as of 06:09, 11 April 2020
Line 3:		Line 3:
	<SX load='6sgc' size='340' side='right' viewer='molstar' caption='[[6sgc]], [[Resolution\|resolution]] 2.80Å' scene=''>		<SX load='6sgc' size='340' side='right' viewer='molstar' caption='[[6sgc]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6sgc]] is a 86 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6SGC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6sgc]] is a 86 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SGC 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>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene>, <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=12A:2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5-MONOPHOSPHATE'>12A</scene>, <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=70U:5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5-MONOPHOSPHATE'>70U</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=12A:2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5-MONOPHOSPHATE'>12A</scene>, <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=70U:5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5-MONOPHOSPHATE'>70U</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=6sgc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sgc OCA], [http://pdbe.org/6sgc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sgc RCSB], [http://www.ebi.ac.uk/pdbsum/6sgc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sgc 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=6sgc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sgc OCA], [http://pdbe.org/6sgc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sgc RCSB], [http://www.ebi.ac.uk/pdbsum/6sgc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sgc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 00:50, 7 March 2020

OCA — Sat, 07 Mar 2020 00:50:34 GMT

←Older revision		Revision as of 00:50, 7 March 2020
Line 1:		Line 1:

	==Rabbit 80S ribosome stalled on a poly(A) tail==		==Rabbit 80S ribosome stalled on a poly(A) tail==
-	<~~StructureSection~~ load='6sgc' size='340' side='right'caption='[[6sgc]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<SX load='6sgc' size='340' side='right' viewer='molstar' caption='[[6sgc]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6sgc]] is a 86 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SGC FirstGlance]. <br>		<table><tr><td colspan='2'>[[6sgc]] is a 86 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SGC FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6sgc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6sgc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: European rabbit]]		[[Category: European rabbit]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 13:14, 18 December 2019

OCA — Wed, 18 Dec 2019 13:14:29 GMT

←Older revision

Revision as of 13:14, 18 December 2019

OCA at 08:17, 4 December 2019

OCA — Wed, 04 Dec 2019 08:17:15 GMT

←Older revision		Revision as of 08:17, 4 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6sgc is ~~ON HOLD~~	+	==Rabbit 80S ribosome stalled on a poly(A) tail==
		+	<StructureSection load='6sgc' size='340' side='right'caption='[[6sgc]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6sgc]] is a 86 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SGC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SGC 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>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene>, <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=12A:2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5-MONOPHOSPHATE'>12A</scene>, <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=70U:5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5-MONOPHOSPHATE'>70U</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=6sgc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sgc OCA], [http://pdbe.org/6sgc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sgc RCSB], [http://www.ebi.ac.uk/pdbsum/6sgc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sgc ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/G1SS70_RABIT G1SS70_RABIT]] May play a role during erythropoiesis through regulation of transcription factor DDIT3.[HAMAP-Rule:MF_03122]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate polyadenylation at near-cognate sites within the coding region. How ribosomes stall selectively when they encounter poly(A) is unclear. Here, we use biochemical and structural approaches in mammalian systems to show that poly-lysine, encoded by poly(A), favors a peptidyl-transfer RNA conformation suboptimal for peptide bond formation. This conformation partially slows elongation, permitting poly(A) mRNA in the ribosome's decoding center to adopt a ribosomal RNA-stabilized single-stranded helix. The reconfigured decoding center clashes with incoming aminoacyl-tRNA, thereby precluding elongation. Thus, coincidence detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs selectively, stall elongation and trigger downstream quality control pathways essential for cellular homeostasis.

-	~~Authors~~:	+	Mechanism of ribosome stalling during translation of a poly(A) tail.,Chandrasekaran V, Juszkiewicz S, Choi J, Puglisi JD, Brown A, Shao S, Ramakrishnan V, Hegde RS Nat Struct Mol Biol. 2019 Nov 25. pii: 10.1038/s41594-019-0331-x. doi:, 10.1038/s41594-019-0331-x. PMID:31768042<ref>PMID:31768042</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6sgc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Oryctolagus cuniculus]]
		+	[[Category: Brown, A]]
		+	[[Category: Chandrasekaran, V]]
		+	[[Category: Choi, J]]
		+	[[Category: Hegde, R S]]
		+	[[Category: Juszkiewicz, S]]
		+	[[Category: Puglisi, J D]]
		+	[[Category: Ramakrishnan, V]]
		+	[[Category: Shao, S]]
		+	[[Category: Polya tail]]
		+	[[Category: Protein translation]]
		+	[[Category: Ribosome]]
		+	[[Category: Ribosome stalling]]

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

OCA — Wed, 14 Aug 2019 15:11:24 GMT

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

←Older revision

Revision as of 15:11, 14 August 2019

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

OCA — Wed, 14 Aug 2019 15:11:23 GMT

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

New page

'''Unreleased structure'''

The entry 6sgc is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]