This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5t4x

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:36, 6 March 2024) (edit) (undo)
 
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]] 1.81&Aring;' scene=''>
+
<StructureSection load='5t4x' size='340' side='right'caption='[[5t4x]], [[Resolution|resolution]] 1.81&Aring;' 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]] 1.81&#8491;</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&reg;/PubMed&reg;, 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]]
+

Current revision

CRYSTAL STRUCTURE OF PDE6D IN APO-STATE

PDB ID 5t4x

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5t4x"
Personal tools