6vfx - Revision history

OCA at 14:37, 6 March 2024

OCA — Wed, 06 Mar 2024 14:37:31 GMT

←Older revision		Revision as of 14:37, 6 March 2024
Line 3:		Line 3:
	<SX load='6vfx' size='340' side='right' viewer='molstar' caption='[[6vfx]], [[Resolution\|resolution]] 2.90Å' scene=''>		<SX load='6vfx' size='340' side='right' viewer='molstar' caption='[[6vfx]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vfx]] is a 21 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/ ] and [~~http~~://en.wikipedia.org/wiki/~~Escherichia_coli_bl21(de3) Escherichia coli bl21(de3)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VFX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vfx]] is a 21 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)] and [https://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VFX 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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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]] 2.9Å</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='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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat">[[6vfs\|6vfs]]</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=6vfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vfx OCA], [https://pdbe.org/6vfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vfx RCSB], [https://www.ebi.ac.uk/pdbsum/6vfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vfx ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92]~~ </~~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=6vfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vfx OCA], [~~http~~://pdbe.org/6vfx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vfx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vfx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vfx ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A0Y4ZJG4_NEIME A0A0Y4ZJG4_NEIME]~~] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.[HAMAP-Rule:MF_00175][SAAS:SAAS01076750] [[http://www.uniprot.org/uniprot/A0A0Y5K536_NEIME A0A0Y5K536_NEIME]] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.[HAMAP-Rule:MF_00444][RuleBase:RU000550][SAAS:SAAS00674840]	+	[https://www.uniprot.org/uniprot/CLPX_NEIMB CLPX_NEIMB] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.[HAMAP-Rule:MF_00175]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ClpXP is an important target for drug development against infectious diseases. Although structures are available for isolated ClpX and ClpP rings, it remains unknown how symmetry mismatched ClpX and ClpP work in tandem for processive substrate translocation into the ClpP proteolytic chamber. Here we present cryo-EM structures of the substrate-bound ClpXP complex from Neisseria meningitidis at 2.3 to 3.3 A resolution. The structures allow development of a model in which the sequential hydrolysis of ATP is coupled to motions of ClpX loops that lead to directional substrate translocation and ClpX rotation relative to ClpP. Our data add to the growing body of evidence that AAA+ molecular machines generate translocating forces by a common mechanism.	+
-		+
-	A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery.,Ripstein ZA, Vahidi S, Houry WA, Rubinstein JL, Kay LE Elife. 2020 Jan 9;9. pii: 52158. doi: 10.7554/eLife.52158. PMID:31916936<ref>PMID:31916936</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6vfx" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Endopeptidase Clp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Houry, W A~~]]	+	[[Category: Neisseria meningitidis]]
-	[[Category: ~~Kay, L E~~]]	+	[[Category: Houry WA]]
-	[[Category: ~~Ripstein, Z A~~]]	+	[[Category: Kay LE]]
-	[[Category: ~~Rubinstein, J L~~]]	+	[[Category: Ripstein ZA]]
-	[[Category: ~~Vahidi, S~~]]	+	[[Category: Rubinstein JL]]
-	[[Category: ~~Aaa+]]~~	+	[[Category: Vahidi S]]
-	~~[[Category: Clpp]]~~	+
-	~~[[Category: Clpx]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protease~~]]	+

OCA at 07:08, 11 April 2020

OCA — Sat, 11 Apr 2020 07:08:54 GMT

←Older revision		Revision as of 07:08, 11 April 2020
Line 3:		Line 3:
	<SX load='6vfx' size='340' side='right' viewer='molstar' caption='[[6vfx]], [[Resolution\|resolution]] 2.90Å' scene=''>		<SX load='6vfx' size='340' side='right' viewer='molstar' caption='[[6vfx]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vfx]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_bl21(de3) Escherichia coli bl21(de3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VFX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6VFX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vfx]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_bl21(de3) Escherichia coli bl21(de3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VFX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VFX 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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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">[[6vfs\|6vfs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6vfs\|6vfs]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </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=6vfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vfx OCA], [http://pdbe.org/6vfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vfx RCSB], [http://www.ebi.ac.uk/pdbsum/6vfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vfx 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=6vfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vfx OCA], [http://pdbe.org/6vfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vfx RCSB], [http://www.ebi.ac.uk/pdbsum/6vfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vfx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 01:25, 7 March 2020

OCA — Sat, 07 Mar 2020 01:25:38 GMT

←Older revision		Revision as of 01:25, 7 March 2020
Line 1:		Line 1:

	==ClpXP from Neisseria meningitidis - Conformation B==		==ClpXP from Neisseria meningitidis - Conformation B==
-	<~~StructureSection~~ load='6vfx' size='340' side='right'caption='[[6vfx]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<SX load='6vfx' size='340' side='right' viewer='molstar' caption='[[6vfx]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6vfx]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_bl21(de3) Escherichia coli bl21(de3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VFX FirstGlance]. <br>		<table><tr><td colspan='2'>[[6vfx]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_bl21(de3) Escherichia coli bl21(de3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VFX FirstGlance]. <br>
Line 24:		Line 24:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Endopeptidase Clp]]		[[Category: Endopeptidase Clp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

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

OCA — Wed, 22 Jan 2020 16:24:05 GMT

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

←Older revision

Revision as of 16:24, 22 January 2020

OCA: New page: ==ClpXP from Neisseria meningitidis - Conformation B== == Structur...

OCA — Wed, 22 Jan 2020 16:24:03 GMT

New page: ==ClpXP from Neisseria meningitidis - Conformation B== <StructureSection load='6vfx' size='340' side='right'caption='6vfx, resolution 2.90Å' scene=''> == Structur...

New page

==ClpXP from Neisseria meningitidis - Conformation B==
<StructureSection load='6vfx' size='340' side='right'caption='[[6vfx]], [[Resolution|resolution]] 2.90Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6vfx]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_bl21(de3) Escherichia coli bl21(de3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VFX 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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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">[[6vfs|6vfs]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </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=6vfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vfx OCA], [http://pdbe.org/6vfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vfx RCSB], [http://www.ebi.ac.uk/pdbsum/6vfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vfx ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/A0A0Y4ZJG4_NEIME A0A0Y4ZJG4_NEIME]] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.[HAMAP-Rule:MF_00175][SAAS:SAAS01076750] [[http://www.uniprot.org/uniprot/A0A0Y5K536_NEIME A0A0Y5K536_NEIME]] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.[HAMAP-Rule:MF_00444][RuleBase:RU000550][SAAS:SAAS00674840]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ClpXP is an important target for drug development against infectious diseases. Although structures are available for isolated ClpX and ClpP rings, it remains unknown how symmetry mismatched ClpX and ClpP work in tandem for processive substrate translocation into the ClpP proteolytic chamber. Here we present cryo-EM structures of the substrate-bound ClpXP complex from Neisseria meningitidis at 2.3 to 3.3 A resolution. The structures allow development of a model in which the sequential hydrolysis of ATP is coupled to motions of ClpX loops that lead to directional substrate translocation and ClpX rotation relative to ClpP. Our data add to the growing body of evidence that AAA+ molecular machines generate translocating forces by a common mechanism.

A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery.,Ripstein ZA, Vahidi S, Houry WA, Rubinstein JL, Kay LE Elife. 2020 Jan 9;9. pii: 52158. doi: 10.7554/eLife.52158. PMID:31916936<ref>PMID:31916936</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6vfx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Endopeptidase Clp]]
[[Category: Large Structures]]
[[Category: Houry, W A]]
[[Category: Kay, L E]]
[[Category: Ripstein, Z A]]
[[Category: Rubinstein, J L]]
[[Category: Vahidi, S]]
[[Category: Aaa+]]
[[Category: Clpp]]
[[Category: Clpx]]
[[Category: Complex]]
[[Category: Hydrolase]]
[[Category: Protease]]