5t4x - Revision history

OCA at 15:36, 6 March 2024

OCA — Wed, 06 Mar 2024 15:36:40 GMT

←Older revision		Revision as of 15:36, 6 March 2024
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF PDE6D IN APO-STATE==		==CRYSTAL STRUCTURE OF PDE6D IN APO-STATE==
-	<StructureSection load='5t4x' size='340' side='right' caption='[[5t4x]], [[Resolution\|resolution]] 1.81Å' scene=''>	+	<StructureSection load='5t4x' size='340' side='right'caption='[[5t4x]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t4x]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T4X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T4X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t4x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T4X FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Pde6d (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10090 LK3 transgenic mice])~~</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]] 1.81Å</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=5t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4x OCA], [~~http~~://pdbe.org/5t4x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t4x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t4x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4x 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=5t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4x OCA], [https://pdbe.org/5t4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t4x RCSB], [https://www.ebi.ac.uk/pdbsum/5t4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PDE6D_MOUSE PDE6D_MOUSE]] Promotes the release of prenylated target proteins from cellular membranes (PubMed:22179043). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22179043). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (By similarity). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (PubMed:22179043). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate.[UniProtKB:O43924][UniProtKB:Q95142]<ref>PMID:10518933</ref> <ref>PMID:15979089</ref> <ref>PMID:22179043</ref>	+	[https://www.uniprot.org/uniprot/PDE6D_MOUSE PDE6D_MOUSE] Promotes the release of prenylated target proteins from cellular membranes (PubMed:22179043). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22179043). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (By similarity). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (PubMed:22179043). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate.[UniProtKB:O43924][UniProtKB:Q95142]<ref>PMID:10518933</ref> <ref>PMID:15979089</ref> <ref>PMID:22179043</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking. Here we report the crystal structure of a solubilization factor, the prenyl-binding protein (PrBP/delta), at 1.81 A resolution in its ligand-free apo-form. Apo-PrBP/delta harbors a preshaped, deep hydrophobic cavity, capacitating apo-PrBP/delta to readily bind its prenylated cargo. To investigate the molecular mechanism of cargo solubilization we analyzed the PrBP/delta-induced membrane dissociation of rod photoreceptor phosphodiesterase (PDE6). The results suggest that PrBP/delta exclusively interacts with the soluble fraction of PDE6. Depletion of soluble species in turn leads to dissociation of membrane-bound PDE6, as both are in equilibrium. This "solubilization by depletion" mechanism of PrBP/delta differs from the extraction of prenylated proteins by the similar folded solubilization factor RhoGDI, which interacts with membrane bound cargo via an N-terminal structural element lacking in PrBP/delta.	+

-	Mechanistic insights into the role of prenyl-binding protein PrBP/delta in membrane dissociation of phosphodiesterase 6.,Qureshi BM, Schmidt A, Behrmann E, Burger J, Mielke T, Spahn CMT, Heck M, Scheerer P Nat Commun. 2018 Jan 8;9(1):90. doi: 10.1038/s41467-017-02569-y. PMID:29311697<ref>PMID:29311697</ref>	+	==See Also==
-		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5t4x" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Qureshi, B M~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Scheerer, P~~]]	+	[[Category: Qureshi BM]]
-	[[Category: ~~Schmidt, A~~]]	+	[[Category: Scheerer P]]
-	[[Category: ~~Apo-state]]~~	+	[[Category: Schmidt A]]
-	~~[[Category: Cellular trafficking]]~~	+
-	~~[[Category: Farnesyl]]~~	+
-	~~[[Category: Geranylgeranyl]]~~	+
-	~~[[Category: Immunoglobulin-like beta sandwitch]]~~	+
-	~~[[Category: Lipid binding protein]]~~	+
-	~~[[Category: Membrane dissociation]]~~	+
-	~~[[Category: Membrane trafficking]]~~	+
-	~~[[Category: Pde6 delta]]~~	+
-	~~[[Category: Phosphodiesterase 6]]~~	+
-	~~[[Category: Prenyl binding protein]]~~	+
-	~~[[Category: Ras-gtpase]]~~	+
-	~~[[Category: Rhodopsin]]~~	+
-	~~[[Category: Rhodopsin kinase]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 08:12, 17 January 2018

OCA — Wed, 17 Jan 2018 08:12:00 GMT

←Older revision		Revision as of 08:12, 17 January 2018
Line 3:		Line 3:
	<StructureSection load='5t4x' size='340' side='right' caption='[[5t4x]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='5t4x' size='340' side='right' caption='[[5t4x]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t4x]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T4X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t4x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T4X FirstGlance]. <br>
-	</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=5t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4x OCA], [http://pdbe.org/5t4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t4x RCSB], [http://www.ebi.ac.uk/pdbsum/5t4x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4x ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pde6d ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4x OCA], [http://pdbe.org/5t4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t4x RCSB], [http://www.ebi.ac.uk/pdbsum/5t4x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PDE6D_MOUSE PDE6D_MOUSE]] Promotes the release of prenylated target proteins from cellular membranes (PubMed:22179043). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22179043). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (By similarity). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (PubMed:22179043). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate.[UniProtKB:O43924][UniProtKB:Q95142]<ref>PMID:10518933</ref> <ref>PMID:15979089</ref> <ref>PMID:22179043</ref>		[[http://www.uniprot.org/uniprot/PDE6D_MOUSE PDE6D_MOUSE]] Promotes the release of prenylated target proteins from cellular membranes (PubMed:22179043). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22179043). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (By similarity). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (PubMed:22179043). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate.[UniProtKB:O43924][UniProtKB:Q95142]<ref>PMID:10518933</ref> <ref>PMID:15979089</ref> <ref>PMID:22179043</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking. Here we report the crystal structure of a solubilization factor, the prenyl-binding protein (PrBP/delta), at 1.81 A resolution in its ligand-free apo-form. Apo-PrBP/delta harbors a preshaped, deep hydrophobic cavity, capacitating apo-PrBP/delta to readily bind its prenylated cargo. To investigate the molecular mechanism of cargo solubilization we analyzed the PrBP/delta-induced membrane dissociation of rod photoreceptor phosphodiesterase (PDE6). The results suggest that PrBP/delta exclusively interacts with the soluble fraction of PDE6. Depletion of soluble species in turn leads to dissociation of membrane-bound PDE6, as both are in equilibrium. This "solubilization by depletion" mechanism of PrBP/delta differs from the extraction of prenylated proteins by the similar folded solubilization factor RhoGDI, which interacts with membrane bound cargo via an N-terminal structural element lacking in PrBP/delta.
		+
		+	Mechanistic insights into the role of prenyl-binding protein PrBP/delta in membrane dissociation of phosphodiesterase 6.,Qureshi BM, Schmidt A, Behrmann E, Burger J, Mielke T, Spahn CMT, Heck M, Scheerer P Nat Commun. 2018 Jan 8;9(1):90. doi: 10.1038/s41467-017-02569-y. PMID:29311697<ref>PMID:29311697</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5t4x" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Qureshi, B M]]		[[Category: Qureshi, B M]]
	[[Category: Scheerer, P]]		[[Category: Scheerer, P]]

OCA at 08:25, 10 January 2018

OCA — Wed, 10 Jan 2018 08:25:34 GMT

←Older revision		Revision as of 08:25, 10 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5t4x ~~is ON HOLD~~	+	==CRYSTAL STRUCTURE OF PDE6D IN APO-STATE==
-		+	<StructureSection load='5t4x' size='340' side='right' caption='[[5t4x]], [[Resolution\|resolution]] 1.81Å' scene=''>
-	~~Authors~~: ~~Qureshi~~, B.M., ~~Schmidt~~, A., ~~Scheerer~~, P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5t4x]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T4X FirstGlance]. <br>
-	~~Description: CRYSTAL STRUCTURE OF PDE6D IN APO-STATE~~	+	</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=5t4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4x OCA], [http://pdbe.org/5t4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t4x RCSB], [http://www.ebi.ac.uk/pdbsum/5t4x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4x ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Qureshi, B.M]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDE6D_MOUSE PDE6D_MOUSE]] Promotes the release of prenylated target proteins from cellular membranes (PubMed:22179043). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22179043). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (By similarity). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (PubMed:22179043). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate.[UniProtKB:O43924][UniProtKB:Q95142]<ref>PMID:10518933</ref> <ref>PMID:15979089</ref> <ref>PMID:22179043</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Qureshi, B M]]
		+	[[Category: Scheerer, P]]
	[[Category: Schmidt, A]]		[[Category: Schmidt, A]]
-	[[Category: ~~Scheerer, P~~]]	+	[[Category: Apo-state]]
		+	[[Category: Cellular trafficking]]
		+	[[Category: Farnesyl]]
		+	[[Category: Geranylgeranyl]]
		+	[[Category: Immunoglobulin-like beta sandwitch]]
		+	[[Category: Lipid binding protein]]
		+	[[Category: Membrane dissociation]]
		+	[[Category: Membrane trafficking]]
		+	[[Category: Pde6 delta]]
		+	[[Category: Phosphodiesterase 6]]
		+	[[Category: Prenyl binding protein]]
		+	[[Category: Ras-gtpase]]
		+	[[Category: Rhodopsin]]
		+	[[Category: Rhodopsin kinase]]
		+	[[Category: Transport protein]]

OCA at 07:58, 4 October 2017

OCA — Wed, 04 Oct 2017 07:58:49 GMT

←Older revision		Revision as of 07:58, 4 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5t4x is ON HOLD ~~until Paper Publication~~	+	The entry 5t4x is ON HOLD

	Authors: Qureshi, B.M., Schmidt, A., Scheerer, P.		Authors: Qureshi, B.M., Schmidt, A., Scheerer, P.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Qureshi, B.M]]		[[Category: Qureshi, B.M]]
-	[[Category: Scheerer, P]]
	[[Category: Schmidt, A]]		[[Category: Schmidt, A]]
		+	[[Category: Scheerer, P]]

OCA at 13:20, 27 September 2017

OCA — Wed, 27 Sep 2017 13:20:51 GMT

←Older revision		Revision as of 13:20, 27 September 2017
Line 7:		Line 7:
	Description: CRYSTAL STRUCTURE OF PDE6D IN APO-STATE		Description: CRYSTAL STRUCTURE OF PDE6D IN APO-STATE
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Scheerer, P]]
	[[Category: Qureshi, B.M]]		[[Category: Qureshi, B.M]]
		+	[[Category: Scheerer, P]]
	[[Category: Schmidt, A]]		[[Category: Schmidt, A]]

OCA at 13:22, 9 March 2017

OCA — Thu, 09 Mar 2017 13:22:05 GMT

←Older revision		Revision as of 13:22, 9 March 2017
Line 7:		Line 7:
	Description: CRYSTAL STRUCTURE OF PDE6D IN APO-STATE		Description: CRYSTAL STRUCTURE OF PDE6D IN APO-STATE
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Qureshi, B.M]]
	[[Category: Scheerer, P]]		[[Category: Scheerer, P]]
		+	[[Category: Qureshi, B.M]]
	[[Category: Schmidt, A]]		[[Category: Schmidt, A]]

OCA: Protected "5t4x" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 15:42:43 GMT

Protected "5t4x" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:42, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t4x is ON HOLD until Paper Publication Authors: Qureshi, B.M., Schmidt, A., Scheerer, P. Description: CRYSTAL STRUCTURE OF PDE6D IN APO-STATE [[Ca...

OCA — Fri, 09 Sep 2016 15:42:41 GMT

New page: '''Unreleased structure''' The entry 5t4x is ON HOLD until Paper Publication Authors: Qureshi, B.M., Schmidt, A., Scheerer, P. Description: CRYSTAL STRUCTURE OF PDE6D IN APO-STATE [[Ca...

New page

'''Unreleased structure'''

The entry 5t4x is ON HOLD until Paper Publication

Authors: Qureshi, B.M., Schmidt, A., Scheerer, P.

Description: CRYSTAL STRUCTURE OF PDE6D IN APO-STATE
[[Category: Unreleased Structures]]
[[Category: Qureshi, B.M]]
[[Category: Scheerer, P]]
[[Category: Schmidt, A]]