7anu - Revision history

OCA at 12:12, 1 February 2024

2024-02-01T12:12:45Z

←Older revision		Revision as of 12:12, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7anu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANU FirstGlance]. <br>		<table><tr><td colspan='2'>[[7anu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.64Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=7anu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anu OCA], [https://pdbe.org/7anu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anu RCSB], [https://www.ebi.ac.uk/pdbsum/7anu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anu 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=7anu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anu OCA], [https://pdbe.org/7anu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anu RCSB], [https://www.ebi.ac.uk/pdbsum/7anu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q9UZY3_PYRAB Q9UZY3_PYRAB]]	+	[https://www.uniprot.org/uniprot/Q9UZY3_PYRAB Q9UZY3_PYRAB]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:21, 8 September 2022

2022-09-08T05:21:00Z

←Older revision		Revision as of 05:21, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7anu' size='340' side='right'caption='[[7anu]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='7anu' size='340' side='right'caption='[[7anu]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7anu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7anu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=7anu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anu OCA], [https://pdbe.org/7anu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anu RCSB], [https://www.ebi.ac.uk/pdbsum/7anu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anu 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=7anu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anu OCA], [https://pdbe.org/7anu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anu RCSB], [https://www.ebi.ac.uk/pdbsum/7anu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anu ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/Q9UZY3_PYRAB Q9UZY3_PYRAB]]
-	The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterized a small orphan protein, Q9UZY3 (UniProt ID), conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (proteasome-activating nucleotidase [PAN]) as bait. X-ray crystallography and small-angle X-ray scattering experiments revealed that the protein is monomeric and adopts a beta-barrel core structure with an oligonucleotide/oligosaccharide-binding (OB)-fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays transfer ribonucleic acid (tRNA)-binding properties. Pull-downs, co-immunoprecipitation and isothermal titration calorimetry (ITC) studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi (Pa) cellular extracts. The protein was therefore named Pbp11, for Proteasome-Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA-processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.	+
-		+
-	Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex.,Hogrel G, Marino-Puertas L, Laurent S, Ibrahim Z, Coves J, Girard E, Gabel F, Fenel D, Daugeron MC, Clouet-d'Orval B, Basta T, Flament D, Franzetti B Mol Microbiol. 2022 May 26. doi: ~~10.1111~~/~~mmi.14948. PMID:35615908<ref>PMID:35615908</ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 7anu" style="background-color:#fffaf0;"><~~/~~div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Franzetti, B~~]]	+	[[Category: Pyrococcus abyssi GE5]]
-	[[Category: ~~Girard, E~~]]	+	[[Category: Franzetti B]]
-	[[Category: ~~Hogrel, G~~]]	+	[[Category: Girard E]]
-	[[Category: ~~Ob-fold]]~~	+	[[Category: Hogrel G]]
-	~~[[Category: Proteasome adaptor]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Trna binding~~]]	+

OCA at 09:51, 22 June 2022

2022-06-22T09:51:20Z

←Older revision		Revision as of 09:51, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of Pyrococcus abyssi Pbp11==		==Crystal structure of Pyrococcus abyssi Pbp11==
-	<StructureSection load='7anu' size='340' side='right'caption='[[7anu]]' scene=''>	+	<StructureSection load='7anu' size='340' side='right'caption='[[7anu]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7anu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANU FirstGlance]. <br>
-	</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=7anu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anu OCA], [https://pdbe.org/7anu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anu RCSB], [https://www.ebi.ac.uk/pdbsum/7anu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anu ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=7anu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anu OCA], [https://pdbe.org/7anu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anu RCSB], [https://www.ebi.ac.uk/pdbsum/7anu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterized a small orphan protein, Q9UZY3 (UniProt ID), conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (proteasome-activating nucleotidase [PAN]) as bait. X-ray crystallography and small-angle X-ray scattering experiments revealed that the protein is monomeric and adopts a beta-barrel core structure with an oligonucleotide/oligosaccharide-binding (OB)-fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays transfer ribonucleic acid (tRNA)-binding properties. Pull-downs, co-immunoprecipitation and isothermal titration calorimetry (ITC) studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi (Pa) cellular extracts. The protein was therefore named Pbp11, for Proteasome-Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA-processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.
		+
		+	Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex.,Hogrel G, Marino-Puertas L, Laurent S, Ibrahim Z, Coves J, Girard E, Gabel F, Fenel D, Daugeron MC, Clouet-d'Orval B, Basta T, Flament D, Franzetti B Mol Microbiol. 2022 May 26. doi: 10.1111/mmi.14948. PMID:35615908<ref>PMID:35615908</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7anu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Franzetti B]]	+	[[Category: Franzetti, B]]
-	[[Category: Girard E]]	+	[[Category: Girard, E]]
-	[[Category: Hogrel G]]	+	[[Category: Hogrel, G]]
		+	[[Category: Ob-fold]]
		+	[[Category: Proteasome adaptor]]
		+	[[Category: Protein binding]]
		+	[[Category: Trna binding]]

OCA at 14:27, 3 November 2021

2021-11-03T14:27:29Z

←Older revision		Revision as of 14:27, 3 November 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7anu ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Pyrococcus abyssi Pbp11==
-		+	<StructureSection load='7anu' size='340' side='right'caption='[[7anu]]' scene=''>
-	~~Authors~~: ~~Hogrel~~, G., ~~Girard~~, E., ~~Franzetti~~, B.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ANU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ANU FirstGlance]. <br>
-	~~Description: Crystal structure of Pyrococcus abyssi Pbp11~~	+	</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=7anu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7anu OCA], [https://pdbe.org/7anu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7anu RCSB], [https://www.ebi.ac.uk/pdbsum/7anu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7anu ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Girard, E~~]]	+	__TOC__
-	[[Category: ~~Hogrel, G~~]]	+	</StructureSection>
-	[[Category: ~~Franzetti, B~~]]	+	[[Category: Large Structures]]
		+	[[Category: Franzetti B]]
		+	[[Category: Girard E]]
		+	[[Category: Hogrel G]]

OCA at 06:14, 11 November 2020

2020-11-11T06:14:10Z

←Older revision		Revision as of 06:14, 11 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7anu is ON HOLD	+	The entry 7anu is ON HOLD until Paper Publication

	Authors: Hogrel, G., Girard, E., Franzetti, B.		Authors: Hogrel, G., Girard, E., Franzetti, B.

OCA: Protected "7anu" [edit=sysop:move=sysop]

2020-10-21T06:37:53Z

Protected "7anu" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:37, 21 October 2020

OCA: New page: '''Unreleased structure''' The entry 7anu is ON HOLD Authors: Hogrel, G., Girard, E., Franzetti, B. Description: Crystal structure of Pyrococcus abyssi Pbp11 [[Category: Unreleased Str...

2020-10-21T06:37:51Z

New page: '''Unreleased structure''' The entry 7anu is ON HOLD Authors: Hogrel, G., Girard, E., Franzetti, B. Description: Crystal structure of Pyrococcus abyssi Pbp11 [[Category: Unreleased Str...

New page

'''Unreleased structure'''

The entry 7anu is ON HOLD

Authors: Hogrel, G., Girard, E., Franzetti, B.

Description: Crystal structure of Pyrococcus abyssi Pbp11
[[Category: Unreleased Structures]]
[[Category: Girard, E]]
[[Category: Hogrel, G]]
[[Category: Franzetti, B]]