7rx9 - Revision history

OCA at 16:40, 18 October 2023

OCA — Wed, 18 Oct 2023 16:40:08 GMT

←Older revision		Revision as of 16:40, 18 October 2023
Line 1:		Line 1:

	==Structure of autoinhibited P-Rex1==		==Structure of autoinhibited P-Rex1==
-	<StructureSection load='7rx9' size='340' side='right'caption='[[7rx9]]' scene=''>	+	<StructureSection load='7rx9' size='340' side='right'caption='[[7rx9]], [[Resolution\|resolution]] 3.22Å' 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=7RX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7rx9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RX9 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=7rx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rx9 OCA], [https://pdbe.org/7rx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rx9 RCSB], [https://www.ebi.ac.uk/pdbsum/7rx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rx9 ProSAT]</span></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]] 3.22Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7rx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rx9 OCA], [https://pdbe.org/7rx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rx9 RCSB], [https://www.ebi.ac.uk/pdbsum/7rx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rx9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref> [https://www.uniprot.org/uniprot/PREX1_HUMAN PREX1_HUMAN] Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol 3,4,5-trisphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	P-Rex (PI(3,4,5)P3-dependent Rac exchanger) guanine nucleotide exchange factors potently activate Rho GTPases. P-Rex guanine nucleotide exchange factors are autoinhibited, synergistically activated by Gbetagamma and PI(3,4,5)P3 binding and dysregulated in cancer. Here, we use X-ray crystallography, cryogenic electron microscopy and crosslinking mass spectrometry to determine the structural basis of human P-Rex1 autoinhibition. P-Rex1 has a bipartite structure of N- and C-terminal modules connected by a C-terminal four-helix bundle that binds the N-terminal Pleckstrin homology (PH) domain. In the N-terminal module, the Dbl homology (DH) domain catalytic surface is occluded by the compact arrangement of the DH-PH-DEP1 domains. Structural analysis reveals a remarkable conformational transition to release autoinhibition, requiring a 126 degrees opening of the DH domain hinge helix. The off-axis position of Gbetagamma and PI(3,4,5)P3 binding sites further suggests a counter-rotation of the P-Rex1 halves by 90 degrees facilitates PH domain uncoupling from the four-helix bundle, releasing the autoinhibited DH domain to drive Rho GTPase signaling.
		+
		+	Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism.,Chang YG, Lupton CJ, Bayly-Jones C, Keen AC, D'Andrea L, Lucato CM, Steele JR, Venugopal H, Schittenhelm RB, Whisstock JC, Halls ML, Ellisdon AM Nat Struct Mol Biol. 2022 Jul 21. pii: 10.1038/s41594-022-00804-9. doi:, 10.1038/s41594-022-00804-9. PMID:35864164<ref>PMID:35864164</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7rx9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia virus T4]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chang Y]]		[[Category: Chang Y]]
	[[Category: Ellisdon AM]]		[[Category: Ellisdon AM]]

OCA at 11:07, 31 August 2022

OCA — Wed, 31 Aug 2022 11:07:02 GMT

←Older revision		Revision as of 11:07, 31 August 2022
Line 1:		Line 1:

	==Structure of autoinhibited P-Rex1==		==Structure of autoinhibited P-Rex1==
-	<StructureSection load='7rx9' size='340' side='right'caption='[[7rx9]]~~, [[Resolution\|resolution]] 3.22Å~~' scene=''>	+	<StructureSection load='7rx9' size='340' side='right'caption='[[7rx9]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7rx9]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RX9 FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>~~	+	</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=7rx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rx9 OCA], [https://pdbe.org/7rx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rx9 RCSB], [https://www.ebi.ac.uk/pdbsum/7rx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rx9 ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=7rx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rx9 OCA], [https://pdbe.org/7rx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rx9 RCSB], [https://www.ebi.ac.uk/pdbsum/7rx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rx9 ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/PREX1_HUMAN PREX1_HUMAN]] Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol 3,4,5-trisphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	P-Rex (PI(3,4,5)P3-dependent Rac exchanger) guanine nucleotide exchange factors potently activate Rho GTPases. P-Rex guanine nucleotide exchange factors are autoinhibited, synergistically activated by Gbetagamma and PI(3,4,5)P3 binding and dysregulated in cancer. Here, we use X-ray crystallography, cryogenic electron microscopy and crosslinking mass spectrometry to determine the structural basis of human P-Rex1 autoinhibition. P-Rex1 has a bipartite structure of N- and C-terminal modules connected by a C-terminal four-helix bundle that binds the N-terminal Pleckstrin homology (PH) domain. In the N-terminal module, the Dbl homology (DH) domain catalytic surface is occluded by the compact arrangement of the DH-PH-DEP1 domains. Structural analysis reveals a remarkable conformational transition to release autoinhibition, requiring a 126 degrees opening of the DH domain hinge helix. The off-axis position of Gbetagamma and PI(3,4,5)P3 binding sites further suggests a counter-rotation of the P-Rex1 halves by 90 degrees facilitates PH domain uncoupling from the four-helix bundle, releasing the autoinhibited DH domain to drive Rho GTPase signaling.
-
-	Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism.,Chang YG, Lupton CJ, Bayly-Jones C, Keen AC, D'Andrea L, Lucato CM, Steele JR, Venugopal H, Schittenhelm RB, Whisstock JC, Halls ML, Ellisdon AM Nat Struct Mol Biol. 2022 Jul 21. pii: 10.1038/s41594-022-00804-9. doi:, 10.1038/s41594-022-00804-9. PMID:35864164<ref>PMID:35864164</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7rx9" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Chang Y]]
-	[[Category: Chang, Y]]	+	[[Category: Ellisdon AM]]
-	[[Category: Ellisdon~~, A M]]~~	+
-	~~[[Category: Cdc42]]~~	+
-	~~[[Category: Cell growth]]~~	+
-	~~[[Category: Gef]]~~	+
-	~~[[Category: P-rex1]]~~	+
-	~~[[Category: P-rex2]]~~	+
-	~~[[Category: Rac1]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 05:13, 25 August 2022

OCA — Thu, 25 Aug 2022 05:13:07 GMT

←Older revision		Revision as of 05:13, 25 August 2022
Line 1:		Line 1:

	==Structure of autoinhibited P-Rex1==		==Structure of autoinhibited P-Rex1==
-	<StructureSection load='7rx9' size='340' side='right'caption='[[7rx9]]' scene=''>	+	<StructureSection load='7rx9' size='340' side='right'caption='[[7rx9]], [[Resolution\|resolution]] 3.22Å' 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=7RX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7rx9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RX9 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=7rx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rx9 OCA], [https://pdbe.org/7rx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rx9 RCSB], [https://www.ebi.ac.uk/pdbsum/7rx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rx9 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=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=7rx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rx9 OCA], [https://pdbe.org/7rx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rx9 RCSB], [https://www.ebi.ac.uk/pdbsum/7rx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rx9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PREX1_HUMAN PREX1_HUMAN]] Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol 3,4,5-trisphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	P-Rex (PI(3,4,5)P3-dependent Rac exchanger) guanine nucleotide exchange factors potently activate Rho GTPases. P-Rex guanine nucleotide exchange factors are autoinhibited, synergistically activated by Gbetagamma and PI(3,4,5)P3 binding and dysregulated in cancer. Here, we use X-ray crystallography, cryogenic electron microscopy and crosslinking mass spectrometry to determine the structural basis of human P-Rex1 autoinhibition. P-Rex1 has a bipartite structure of N- and C-terminal modules connected by a C-terminal four-helix bundle that binds the N-terminal Pleckstrin homology (PH) domain. In the N-terminal module, the Dbl homology (DH) domain catalytic surface is occluded by the compact arrangement of the DH-PH-DEP1 domains. Structural analysis reveals a remarkable conformational transition to release autoinhibition, requiring a 126 degrees opening of the DH domain hinge helix. The off-axis position of Gbetagamma and PI(3,4,5)P3 binding sites further suggests a counter-rotation of the P-Rex1 halves by 90 degrees facilitates PH domain uncoupling from the four-helix bundle, releasing the autoinhibited DH domain to drive Rho GTPase signaling.
		+
		+	Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism.,Chang YG, Lupton CJ, Bayly-Jones C, Keen AC, D'Andrea L, Lucato CM, Steele JR, Venugopal H, Schittenhelm RB, Whisstock JC, Halls ML, Ellisdon AM Nat Struct Mol Biol. 2022 Jul 21. pii: 10.1038/s41594-022-00804-9. doi:, 10.1038/s41594-022-00804-9. PMID:35864164<ref>PMID:35864164</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7rx9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang Y]]	+	[[Category: Lysozyme]]
-	[[Category: Ellisdon AM]]	+	[[Category: Chang, Y]]
		+	[[Category: Ellisdon, A M]]
		+	[[Category: Cdc42]]
		+	[[Category: Cell growth]]
		+	[[Category: Gef]]
		+	[[Category: P-rex1]]
		+	[[Category: P-rex2]]
		+	[[Category: Rac1]]
		+	[[Category: Signaling protein]]

OCA at 05:00, 10 August 2022

OCA — Wed, 10 Aug 2022 05:00:03 GMT

←Older revision		Revision as of 05:00, 10 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7rx9 ~~is ON HOLD until Paper Publication~~	+	==Structure of autoinhibited P-Rex1==
-		+	<StructureSection load='7rx9' size='340' side='right'caption='[[7rx9]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RX9 FirstGlance]. <br>
-	~~Description~~:	+	</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=7rx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rx9 OCA], [https://pdbe.org/7rx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rx9 RCSB], [https://www.ebi.ac.uk/pdbsum/7rx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rx9 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chang Y]]
		+	[[Category: Ellisdon AM]]

OCA at 04:11, 6 October 2021

OCA — Wed, 06 Oct 2021 04:11:16 GMT

←Older revision		Revision as of 04:11, 6 October 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7rx9 is ON HOLD	+	The entry 7rx9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7rx9" [edit=sysop:move=sysop]

OCA — Wed, 08 Sep 2021 07:46:42 GMT

Protected "7rx9" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:46, 8 September 2021

OCA: New page: '''Unreleased structure''' The entry 7rx9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Sep 2021 07:46:41 GMT

New page: '''Unreleased structure''' The entry 7rx9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7rx9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]