5t6r - Revision history

OCA at 14:08, 13 March 2024

OCA — Wed, 13 Mar 2024 14:08:36 GMT

←Older revision		Revision as of 14:08, 13 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5t6r]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T6R FirstGlance]. <br>		<table><tr><td colspan='2'>[[5t6r]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 4.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [https://pdbe.org/5t6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [https://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r 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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [https://pdbe.org/5t6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [https://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RL7A_YEAST RL7A_YEAST]		[https://www.uniprot.org/uniprot/RL7A_YEAST RL7A_YEAST]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position. Additional domains occupy the P site and extend toward the sarcin-ricin loop to interact with Tif6. Nmd3 and Lsg1 together embrace helix 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase activity of Lsg1.
-
-	Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.,Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW EMBO J. 2017 Feb 8. pii: e201696012. doi: 10.15252/embj.201696012. PMID:28179369<ref>PMID:28179369</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5t6r" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribosome 3D structures\|Ribosome 3D structures]]		*[[Ribosome 3D structures\|Ribosome 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>

OCA at 04:31, 30 September 2022

OCA — Fri, 30 Sep 2022 04:31:46 GMT

←Older revision		Revision as of 04:31, 30 September 2022
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	<SX load='5t6r' size='340' side='right' viewer='molstar' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>		<SX load='5t6r' size='340' side='right' viewer='molstar' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]], [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast~~] 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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5T6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t6r]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [https://pdbe.org/5t6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [https://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t62\|5t62]]</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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [~~http~~://pdbe.org/5t6r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~RL5_YEAST RL5_YEAST~~]] Binds 5S RNA and is required for 60S subunit assembly. [[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/RL11A_YEAST RL11A_YEAST]] Binds to 5S ribosomal RNA. [[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/RL401_YEAST RL401_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).<ref>PMID:23169626</ref> 60S ribosomal protein L40: component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2.<ref>PMID:23169626</ref> [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity).	+	[https://www.uniprot.org/uniprot/RL7A_YEAST RL7A_YEAST]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Frank, J]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Johnson~~, A W~~]]	+	[[Category: Frank J]]
-	[[Category: Malyutin~~, A G~~]]	+	[[Category: Johnson AW]]
-	[[Category: Musalgaonkar, S]]	+	[[Category: Malyutin AG]]
-	[[Category: Patchett, S]]	+	[[Category: Musalgaonkar S]]
-	~~[[Category: Cryo-em]]~~	+	[[Category: Patchett S]]
-	~~[[Category: Lsg1]]~~	+
-	~~[[Category: Nmd3]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Ribosome biogenesis]]~~	+
-	~~[[Category: Tif6~~]]	+

OCA at 21:37, 10 April 2020

OCA — Fri, 10 Apr 2020 21:37:47 GMT

←Older revision		Revision as of 21:37, 10 April 2020
Line 3:		Line 3:
	<SX load='5t6r' size='340' side='right' viewer='molstar' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>		<SX load='5t6r' size='340' side='right' viewer='molstar' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]], [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] 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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]], [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] 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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t62\|5t62]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t62\|5t62]]</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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [http://pdbe.org/5t6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [http://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r 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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [http://pdbe.org/5t6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [http://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:34, 6 March 2020

OCA — Fri, 06 Mar 2020 19:34:13 GMT

←Older revision		Revision as of 19:34, 6 March 2020
Line 1:		Line 1:

	==Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex==		==Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex==
-	<~~StructureSection~~ load='5t6r' size='340' side='right'caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>	+	<SX load='5t6r' size='340' side='right' viewer='molstar' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]], [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] 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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6R FirstGlance]. <br>		<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]], [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] 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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5t6r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5t6r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 16:42, 20 November 2019

OCA — Wed, 20 Nov 2019 16:42:16 GMT

←Older revision		Revision as of 16:42, 20 November 2019
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex==		==Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex==
-	<StructureSection load='5t6r' size='340' side='right' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>	+	<StructureSection load='5t6r' size='340' side='right'caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~], [http://en.wikipedia.org/wiki/~~Dsm_2053 Dsm 2053~~] 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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]], [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] 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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=UNK:UNKNOWN'>UNK</scene></td></tr>
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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [http://pdbe.org/5t6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [http://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r 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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [http://pdbe.org/5t6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [http://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[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/RL11A_YEAST RL11A_YEAST]] Binds to 5S ribosomal RNA. [[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/RL401_YEAST RL401_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).<ref>PMID:23169626</ref> 60S ribosomal protein L40: component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2.<ref>PMID:23169626</ref> [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity).		[[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[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/RL11A_YEAST RL11A_YEAST]] Binds to 5S ribosomal RNA. [[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/RL401_YEAST RL401_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).<ref>PMID:23169626</ref> 60S ribosomal protein L40: component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2.<ref>PMID:23169626</ref> [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity).
Line 26:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
-	[[Category: ~~Dsm 2053~~]]	+	[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Frank, J]]		[[Category: Frank, J]]

OCA at 10:33, 8 November 2017

OCA — Wed, 08 Nov 2017 10:33:38 GMT

←Older revision		Revision as of 10:33, 8 November 2017
Line 3:		Line 3:
	<StructureSection load='5t6r' size='340' side='right' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>		<StructureSection load='5t6r' size='340' side='right' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~] ~~and~~ [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae_(strain_atcc_204508_~~/~~_s288c)~~ Saccharomyces cerevisiae ~~(strain atcc 204508 / s288c)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast], [http://en.wikipedia.org/wiki/Dsm_2053 Dsm 2053] 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=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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=UNK:UNKNOWN'>UNK</scene></td></tr>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
		+	[[Category: Dsm 2053]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Frank, J]]		[[Category: Frank, J]]

OCA at 08:27, 9 March 2017

OCA — Thu, 09 Mar 2017 08:27:20 GMT

←Older revision		Revision as of 08:27, 9 March 2017
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	{{Large structure}}
		+	==Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex==
		+	<StructureSection load='5t6r' size='340' side='right' caption='[[5t6r]], [[Resolution\|resolution]] 4.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5t6r]] is a 45 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_atcc_204508_/_s288c) Saccharomyces cerevisiae (strain atcc 204508 / s288c)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6R FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t62\|5t62]]</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=5t6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6r OCA], [http://pdbe.org/5t6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6r RCSB], [http://www.ebi.ac.uk/pdbsum/5t6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6r ProSAT]</span></td></tr>
		+	</table>
		+	{{Large structure}}
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RL5_YEAST RL5_YEAST]] Binds 5S RNA and is required for 60S subunit assembly. [[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/RL11A_YEAST RL11A_YEAST]] Binds to 5S ribosomal RNA. [[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/RL401_YEAST RL401_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).<ref>PMID:23169626</ref> 60S ribosomal protein L40: component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2.<ref>PMID:23169626</ref> [[http://www.uniprot.org/uniprot/RL37A_YEAST RL37A_YEAST]] Binds to the 23S rRNA (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position. Additional domains occupy the P site and extend toward the sarcin-ricin loop to interact with Tif6. Nmd3 and Lsg1 together embrace helix 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase activity of Lsg1.

-	~~The entry 5t6r~~ is ~~ON HOLD until Paper Publication~~	+	Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.,Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW EMBO J. 2017 Feb 8. pii: e201696012. doi: 10.15252/embj.201696012. PMID:28179369<ref>PMID:28179369</ref>

-	~~Authors~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	<div class="pdbe-citations 5t6r" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Frank, J]]
		+	[[Category: Johnson, A W]]
		+	[[Category: Malyutin, A G]]
		+	[[Category: Musalgaonkar, S]]
		+	[[Category: Patchett, S]]
		+	[[Category: Cryo-em]]
		+	[[Category: Lsg1]]
		+	[[Category: Nmd3]]
		+	[[Category: Ribosome]]
		+	[[Category: Ribosome biogenesis]]
		+	[[Category: Tif6]]

OCA at 17:16, 9 December 2016

OCA — Fri, 09 Dec 2016 17:16:13 GMT

←Older revision		Revision as of 17:16, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5t6r is ON HOLD	+	The entry 5t6r is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5t6r" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 15:48:29 GMT

Protected "5t6r" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:48, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t6r is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Sep 2016 15:48:28 GMT

New page: '''Unreleased structure''' The entry 5t6r is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5t6r is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]