4n5c: Difference between revisions

Revision as of 10:36, 28 December 2022

Crystal structure of Ypp1

Structural highlights

4n5c is a 8 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YPP1_YEAST Involved in endocytosis.^[1]

Publication Abstract from PubMed

Plasma membrane PI4P helps determine the identity of this membrane and plays a key role in signal transduction as the precursor of PI(4,5)P2 and its metabolites. Here, we report the atomic structure of the protein scaffold that is required for the plasma membrane localization and function of Stt4/PI4KIIIalpha, the PI 4-kinase responsible for this PI4P pool. Both proteins of the scaffold, Efr3 and YPP1/TTC7, are composed of alpha-helical repeats, which are arranged into a rod in Efr3 and a superhelix in Ypp1. A conserved basic patch in Efr3, which binds acidic phospholipids, anchors the complex to the plasma membrane. Stt4/PI4KIIIalpha is recruited by interacting with the Ypp1 C-terminal lobe, which also binds to unstructured regions in the Efr3 C terminus. Phosphorylation of this Efr3 region counteracts Ypp1 binding, thus providing a mechanism through which Stt4/PI4KIIIalpha recruitment, and thus a metabolic reaction of fundamental importance in cell physiology, can be regulated.

Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex.,Wu X, Chi RJ, Baskin JM, Lucast L, Burd CG, De Camilli P, Reinisch KM Dev Cell. 2014 Jan 13;28(1):19-29. doi: 10.1016/j.devcel.2013.11.012. Epub 2013, Dec 19. PMID:24360784^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Flower TR, Clark-Dixon C, Metoyer C, Yang H, Shi R, Zhang Z, Witt SN. YGR198w (YPP1) targets A30P alpha-synuclein to the vacuole for degradation. J Cell Biol. 2007 Jun 18;177(6):1091-104. PMID:17576801 doi:https://dx.doi.org/10.1083/jcb.200610071
↑ Wu X, Chi RJ, Baskin JM, Lucast L, Burd CG, De Camilli P, Reinisch KM. Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex. Dev Cell. 2014 Jan 13;28(1):19-29. doi: 10.1016/j.devcel.2013.11.012. Epub 2013, Dec 19. PMID:24360784 doi:https://dx.doi.org/10.1016/j.devcel.2013.11.012

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Flower TR, Clark-Dixon C, Metoyer C, Yang H, Shi R, Zhang Z, Witt SN. YGR198w (YPP1) targets A30P alpha-synuclein to the vacuole for degradation. J Cell Biol. 2007 Jun 18;177(6):1091-104. PMID:17576801 doi:https://dx.doi.org/10.1083/jcb.200610071

[2] Wu X, Chi RJ, Baskin JM, Lucast L, Burd CG, De Camilli P, Reinisch KM. Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex. Dev Cell. 2014 Jan 13;28(1):19-29. doi: 10.1016/j.devcel.2013.11.012. Epub 2013, Dec 19. PMID:24360784 doi:https://dx.doi.org/10.1016/j.devcel.2013.11.012

[1]

[2]

@@ Line 1: / Line 1: @@
-{{Large structure}}
 ==Crystal structure of Ypp1==
-<StructureSection load='4n5c' size='340' side='right' caption='[[4n5c]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
+<StructureSection load='4n5c' size='340' side='right'caption='[[4n5c]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4n5c]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N5C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4n5c]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N5C FirstGlance]. <br>
-</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>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4n5a|4n5a]]</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=4n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n5c OCA], [https://pdbe.org/4n5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n5c RCSB], [https://www.ebi.ac.uk/pdbsum/4n5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n5c ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YPP1, YGR198W, G7594 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n5c OCA], [http://pdbe.org/4n5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n5c RCSB], [http://www.ebi.ac.uk/pdbsum/4n5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n5c ProSAT]</span></td></tr>
 </table>
-{{Large structure}}
 == Function ==
-[[http://www.uniprot.org/uniprot/YPP1_YEAST YPP1_YEAST]] Involved in endocytosis.<ref>PMID:17576801</ref>
+[https://www.uniprot.org/uniprot/YPP1_YEAST YPP1_YEAST] Involved in endocytosis.<ref>PMID:17576801</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
+[[Category: Large Structures]]
-[[Category: Baskin, J M]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Burd, C G]]
+[[Category: Baskin JM]]
-[[Category: Camilli, P De]]
+[[Category: Burd CG]]
-[[Category: Chi, R J]]
+[[Category: Chi RJ]]
-[[Category: Lucast, L]]
+[[Category: De Camilli P]]
-[[Category: Reinisch, K M]]
+[[Category: Lucast L]]
-[[Category: Wu, X]]
+[[Category: Reinisch KM]]
-[[Category: Component of stt4 complex]]
+[[Category: Wu X]]
-[[Category: Efr3]]
-[[Category: Heat-like repeat]]
-[[Category: Plasma membrane]]
-[[Category: Protein binding]]
-[[Category: Stt4]]

4n5c: Difference between revisions

Revision as of 10:36, 28 December 2022

Crystal structure of Ypp1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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