5iet - Revision history

OCA at 13:48, 30 August 2023

OCA — Wed, 30 Aug 2023 13:48:51 GMT

←Older revision		Revision as of 13:48, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='5iet' size='340' side='right'caption='[[5iet]], [[Resolution\|resolution]] 2.88Å' scene=''>		<StructureSection load='5iet' size='340' side='right'caption='[[5iet]], [[Resolution\|resolution]] 2.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iet]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IET OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IET FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iet]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IET FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MPD:(4S)~~-2~~-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.88Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat">[[5ieu\|5ieu]]</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=5iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iet OCA], [https://pdbe.org/5iet PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iet RCSB], [https://www.ebi.ac.uk/pdbsum/5iet PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iet ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">AFL40_3934 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])~~</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=5iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iet OCA], [~~http~~://pdbe.org/5iet PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5iet RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5iet PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5iet ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BPA_MYCTU BPA_MYCTU] Interacts with the core proteasome alpha-subunit (PrcA) through its C-terminal hydrophobic-tyrosine-X motif (HbYX motif). Interaction of Bpa with the proteasome stimulates proteosomal peptidase and casein degradation activity, which suggests Bpa could play a role in the removal of non-native or damaged proteins by influencing the conformation of the proteasome complex upon interaction. Can inhibit degradation of Pup-tagged substrates in vitro by competing with Mpa for association with the proteasome.<ref>PMID:25469515</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bai, L]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Darwin~~, K H~~]]	+	[[Category: Bai L]]
-	[[Category: Hu, K]]	+	[[Category: Darwin KH]]
-	[[Category: Jastrab~~, J B~~]]	+	[[Category: Hu K]]
-	[[Category: Li, H]]	+	[[Category: Jastrab JB]]
-	[[Category: Wang, T]]	+	[[Category: Li H]]
-	~~[[Category: Activator]]~~	+	[[Category: Wang T]]
-	~~[[Category: Apoptosis]]~~	+
-	~~[[Category: Gene regulation~~]]	+

OCA at 16:16, 11 December 2019

OCA — Wed, 11 Dec 2019 16:16:57 GMT

←Older revision		Revision as of 16:16, 11 December 2019
Line 1:		Line 1:

	==Crystal Structure of Mycobacterium Tuberculosis ATP-independent Proteasome activator==		==Crystal Structure of Mycobacterium Tuberculosis ATP-independent Proteasome activator==
-	<StructureSection load='5iet' size='340' side='right' caption='[[5iet]], [[Resolution\|resolution]] 2.88Å' scene=''>	+	<StructureSection load='5iet' size='340' side='right'caption='[[5iet]], [[Resolution\|resolution]] 2.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iet]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IET FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iet]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IET FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieu\|5ieu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieu\|5ieu]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AFL40_3934 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=5iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iet OCA], [http://pdbe.org/5iet PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iet RCSB], [http://www.ebi.ac.uk/pdbsum/5iet PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iet 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=5iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iet OCA], [http://pdbe.org/5iet PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iet RCSB], [http://www.ebi.ac.uk/pdbsum/5iet PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iet ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bai, L]]		[[Category: Bai, L]]
	[[Category: Darwin, K H]]		[[Category: Darwin, K H]]

OCA at 17:54, 12 July 2016

OCA — Tue, 12 Jul 2016 17:54:56 GMT

←Older revision		Revision as of 17:54, 12 July 2016
Line 7:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieu\|5ieu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieu\|5ieu]]</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=5iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iet OCA], [http://pdbe.org/5iet PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iet RCSB], [http://www.ebi.ac.uk/pdbsum/5iet 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=5iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iet OCA], [http://pdbe.org/5iet PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iet RCSB], [http://www.ebi.ac.uk/pdbsum/5iet PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iet ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:09, 10 May 2016

OCA — Tue, 10 May 2016 19:09:25 GMT

←Older revision		Revision as of 19:09, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5iet is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Mycobacterium Tuberculosis ATP-independent Proteasome activator==
		+	<StructureSection load='5iet' size='340' side='right' caption='[[5iet]], [[Resolution\|resolution]] 2.88Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5iet]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IET FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ieu\|5ieu]]</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=5iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iet OCA], [http://pdbe.org/5iet PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iet RCSB], [http://www.ebi.ac.uk/pdbsum/5iet PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human pathogenMycobacterium tuberculosis(Mtb) requires a proteasome system to cause lethal infections in mice. We recently found that proteasome accessory factor E (PafE, Rv3780) activates proteolysis by theMtbproteasome independently of adenosine triphosphate (ATP). Moreover, PafE contributes to the heat-shock response and virulence ofMtb Here, we show that PafE subunits formed four-helix bundles similar to those of the eukaryotic ATP-independent proteasome activator subunits of PA26 and PA28. However, unlike any other known proteasome activator, PafE formed dodecamers with 12-fold symmetry, which required a glycine-XXX-glycine-XXX-glycine motif that is not found in previously described activators. Intriguingly, the truncation of the PafE carboxyl-terminus resulted in the robust binding of PafE rings to native proteasome core particles and substantially increased proteasomal activity, suggesting that the extended carboxyl-terminus of this cofactor confers suboptimal binding to the proteasome core particle. Collectively, our data show that proteasomal activation is not limited to hexameric ATPases in bacteria.

-	~~Authors:~~ Bai, L., Hu, K., Wang, T., Jastrab~~, J.B.~~, Darwin~~, K.H.~~, Li, H.	+	Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis.,Bai L, Hu K, Wang T, Jastrab JM, Darwin KH, Li H Proc Natl Acad Sci U S A. 2016 Mar 21. pii: 201512094. PMID:27001842<ref>PMID:27001842</ref>

-	~~Description: Crystal Structure~~ of ~~Mycobacterium Tuberculosis ATP-independent Proteasome activator~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Wang, T]]~~	+	<div class="pdbe-citations 5iet" style="background-color:#fffaf0;"></div>
-	~~[[Category: Darwin, K.H]]~~	+	== References ==
-	~~[[Category: Jastrab, J.B]]~~	+	<references/>
-	~~[[Category: Li, H]]~~	+	__TOC__
-	~~[[Category: Hu, K]]~~	+	</StructureSection>
	[[Category: Bai, L]]		[[Category: Bai, L]]
		+	[[Category: Darwin, K H]]
		+	[[Category: Hu, K]]
		+	[[Category: Jastrab, J B]]
		+	[[Category: Li, H]]
		+	[[Category: Wang, T]]
		+	[[Category: Activator]]
		+	[[Category: Apoptosis]]
		+	[[Category: Gene regulation]]

OCA at 02:12, 10 March 2016

OCA — Thu, 10 Mar 2016 02:12:21 GMT

←Older revision		Revision as of 02:12, 10 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Bai, L., Hu, K., Wang, T., Jastrab, J.B., Darwin, K.H., Li, H.		Authors: Bai, L., Hu, K., Wang, T., Jastrab, J.B., Darwin, K.H., Li, H.

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

OCA — Wed, 02 Mar 2016 13:51:47 GMT

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

←Older revision

Revision as of 13:51, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5iet is ON HOLD Authors: Bai, L., Hu, K., Wang, T., Jastrab, J.B., Darwin, K.H., Li, H. Description: Crystal Structure of Mycobacterium Tuberculosi...

OCA — Wed, 02 Mar 2016 13:51:46 GMT

New page: '''Unreleased structure''' The entry 5iet is ON HOLD Authors: Bai, L., Hu, K., Wang, T., Jastrab, J.B., Darwin, K.H., Li, H. Description: Crystal Structure of Mycobacterium Tuberculosi...

New page

'''Unreleased structure'''

The entry 5iet is ON HOLD

Authors: Bai, L., Hu, K., Wang, T., Jastrab, J.B., Darwin, K.H., Li, H.

Description: Crystal Structure of Mycobacterium Tuberculosis ATP-independent Proteasome activator
[[Category: Unreleased Structures]]
[[Category: Wang, T]]
[[Category: Darwin, K.H]]
[[Category: Jastrab, J.B]]
[[Category: Li, H]]
[[Category: Hu, K]]
[[Category: Bai, L]]