3jai - Revision history

OCA at 08:42, 7 February 2024

OCA — Wed, 07 Feb 2024 08:42:14 GMT

←Older revision		Revision as of 08:42, 7 February 2024
Line 3:		Line 3:
	<SX load='3jai' size='340' side='right' viewer='molstar' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>		<SX load='3jai' size='340' side='right' viewer='molstar' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jai]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JAI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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">Electron Microscopy, [[Resolution\|Resolution]] 3.65Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3jag\|3jag]], [[3jah\|3jah]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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">eRF1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])~~</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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [https://pdbe.org/3jai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [https://www.ebi.ac.uk/pdbsum/3jai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai 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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [https://pdbe.org/3jai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [https://www.ebi.ac.uk/pdbsum/3jai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~U3KPD5_RABIT U3KPD5_RABIT~~]] Binds to the 23S rRNA.[RuleBase:RU000576] [[https://www.uniprot.org/uniprot/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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]	+	[https://www.uniprot.org/uniprot/G1TT27_RABIT G1TT27_RABIT]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 A resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination.	+
-		+
-	Structural basis for stop codon recognition in eukaryotes.,Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan V Nature. 2015 Aug 27;524(7566):493-6. doi: 10.1038/nature14896. Epub 2015 Aug 5. PMID:26245381<ref>PMID:26245381</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3jai" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]		*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: European rabbit]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Oryctolagus cuniculus]]		[[Category: Oryctolagus cuniculus]]
-	[[Category: Brown, A]]	+	[[Category: Brown A]]
-	[[Category: Hegde~~, R S~~]]	+	[[Category: Hegde RS]]
-	[[Category: Murray, J]]	+	[[Category: Murray J]]
-	[[Category: Ramakrishnan, V]]	+	[[Category: Ramakrishnan V]]
-	[[Category: Shao, S]]	+	[[Category: Shao S]]
-	~~[[Category: Abce1]]~~	+
-	~~[[Category: Erf1]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Termination~~]]	+

OCA at 13:29, 4 May 2022

OCA — Wed, 04 May 2022 13:29:53 GMT

←Older revision		Revision as of 13:29, 4 May 2022
Line 3:		Line 3:
	<SX load='3jai' size='340' side='right' viewer='molstar' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>		<SX load='3jai' size='340' side='right' viewer='molstar' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3JAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JAI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jag\|3jag]], [[3jah\|3jah]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3jag\|3jag]], [[3jah\|3jah]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">eRF1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">eRF1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [~~http~~://pdbe.org/3jai PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3jai PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai 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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [https://pdbe.org/3jai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [https://www.ebi.ac.uk/pdbsum/3jai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai 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/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[~~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/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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 18:20, 10 April 2020

OCA — Fri, 10 Apr 2020 18:20:32 GMT

←Older revision		Revision as of 18:20, 10 April 2020
Line 3:		Line 3:
	<SX load='3jai' size='340' side='right' viewer='molstar' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>		<SX load='3jai' size='340' side='right' viewer='molstar' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3JAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3JAI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jag\|3jag]], [[3jah\|3jah]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jag\|3jag]], [[3jah\|3jah]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">eRF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">eRF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://pdbe.org/3jai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai 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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://pdbe.org/3jai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 17:35, 6 March 2020

OCA — Fri, 06 Mar 2020 17:35:02 GMT

←Older revision		Revision as of 17:35, 6 March 2020
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codon==		==Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codon==
-	<~~StructureSection~~ load='3jai' size='340' side='right' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>	+	<SX load='3jai' size='340' side='right' viewer='molstar' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAI FirstGlance]. <br>		<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAI FirstGlance]. <br>
Line 9:		Line 9:
	<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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://pdbe.org/3jai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai 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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://pdbe.org/3jai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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]		[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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]
Line 23:		Line 22:

	==See Also==		==See Also==
-	*[[~~TRNA~~\|~~TRNA~~]]	+	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: European rabbit]]		[[Category: European rabbit]]
		+	[[Category: Large Structures]]
	[[Category: Oryctolagus cuniculus]]		[[Category: Oryctolagus cuniculus]]
	[[Category: Brown, A]]		[[Category: Brown, A]]

OCA at 08:23, 18 July 2018

OCA — Wed, 18 Jul 2018 08:23:00 GMT

←Older revision		Revision as of 08:23, 18 July 2018
Line 1:		Line 1:
		+	{{Large structure}}
	==Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codon==		==Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codon==
	<StructureSection load='3jai' size='340' side='right' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>		<StructureSection load='3jai' size='340' side='right' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jag\|3jag]], [[3jah\|3jah]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jag\|3jag]], [[3jah\|3jah]]</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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">eRF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://pdbe.org/3jai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jai ProSAT]</span></td></tr>
	</table>		</table>
	{{Large structure}}		{{Large structure}}
Line 18:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3jai" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA\|TRNA]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: European rabbit]]
	[[Category: Oryctolagus cuniculus]]		[[Category: Oryctolagus cuniculus]]
	[[Category: Brown, A]]		[[Category: Brown, A]]

OCA at 06:33, 2 September 2015

OCA — Wed, 02 Sep 2015 06:33:38 GMT

←Older revision		Revision as of 06:33, 2 September 2015
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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]		[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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 ==
		+	Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 A resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination.
		+
		+	Structural basis for stop codon recognition in eukaryotes.,Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan V Nature. 2015 Aug 27;524(7566):493-6. doi: 10.1038/nature14896. Epub 2015 Aug 5. PMID:26245381<ref>PMID:26245381</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:43, 1 September 2015

OCA — Tue, 01 Sep 2015 13:43:05 GMT

←Older revision		Revision as of 13:43, 1 September 2015
Line 7:		Line 7:
	<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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum]</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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum]</span></td></tr>
	</table>		</table>
		+	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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]		[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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]

OCA at 14:57, 12 August 2015

OCA — Wed, 12 Aug 2015 14:57:36 GMT

←Older revision		Revision as of 14:57, 12 August 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codon==
-		+	<StructureSection load='3jai' size='340' side='right' caption='[[3jai]], [[Resolution\|resolution]] 3.65Å' scene=''>
-	~~The entry~~ 3jai is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3jai]] is a 87 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=3JAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JAI FirstGlance]. <br>
-	~~Authors~~: ~~Brown~~, A., ~~Shao~~, S., ~~Murray, J~~., ~~Hegde, R~~.S., ~~Ramakrishnan, V~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jag\|3jag]], [[3jah\|3jah]]</td></tr>
-	~~Description~~: ~~Structure of a mammalian ribosomal~~ termination ~~complex with ABCE1, eRF1~~(~~AAQ~~), and ~~the~~ UGA stop ~~codon~~	+	<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=3jai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3jai RCSB], [http://www.ebi.ac.uk/pdbsum/3jai PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/ERF1_HUMAN ERF1_HUMAN]] Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.<ref>PMID:7990965</ref> [[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]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Oryctolagus cuniculus]]
	[[Category: Brown, A]]		[[Category: Brown, A]]
-	[[Category: ~~Shao~~, S]]	+	[[Category: Hegde, R S]]
	[[Category: Murray, J]]		[[Category: Murray, J]]
-	[[Category: Hegde, R.S]]
	[[Category: Ramakrishnan, V]]		[[Category: Ramakrishnan, V]]
		+	[[Category: Shao, S]]
		+	[[Category: Abce1]]
		+	[[Category: Erf1]]
		+	[[Category: Ribosome]]
		+	[[Category: Termination]]

OCA: Protected "3jai" [edit=sysop:move=sysop]

OCA — Wed, 24 Jun 2015 07:24:34 GMT

Protected "3jai" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:24, 24 June 2015

OCA: New page: '''Unreleased structure''' The entry 3jai is ON HOLD Authors: Brown, A., Shao, S., Murray, J., Hegde, R.S., Ramakrishnan, V. Description: Structure of a mammalian ribosomal termination...

OCA — Wed, 24 Jun 2015 07:24:32 GMT

New page: '''Unreleased structure''' The entry 3jai is ON HOLD Authors: Brown, A., Shao, S., Murray, J., Hegde, R.S., Ramakrishnan, V. Description: Structure of a mammalian ribosomal termination...

New page

'''Unreleased structure'''

The entry 3jai is ON HOLD

Authors: Brown, A., Shao, S., Murray, J., Hegde, R.S., Ramakrishnan, V.

Description: Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codon
[[Category: Unreleased Structures]]
[[Category: Brown, A]]
[[Category: Shao, S]]
[[Category: Murray, J]]
[[Category: Hegde, R.S]]
[[Category: Ramakrishnan, V]]