8izf: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 8izf is ~~ON HOLD until 2025~~-04-07

==Cryo-EM structure of the Lac1-Lip1 (Lip1-S74F) complex==

== Structural highlights ==

<table><tr><td colspan='2'>[[8izf]] is a 4 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=8IZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IZF FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.85Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PL:(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM+4-OXIDE'>6PL</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=8izf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8izf OCA], [https://pdbe.org/8izf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8izf RCSB], [https://www.ebi.ac.uk/pdbsum/8izf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8izf ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/LAC1_YEAST LAC1_YEAST] Component of the ceramide synthase complex that catalyzes the transfer of the acyl chain from acyl-CoA to a sphingoid base, with high selectivity toward hexacosanoyl-CoA (C26:0-CoA) (PubMed:15692566, PubMed:11694577). N-acylates sphinganine and phytosphingosine bases to form dihydroceramides and phytoceramides, respectively (PubMed:15692566, PubMed:11694577). Redundant with LAG1. Facilitates ER-to-Golgi transport of GPI-anchored proteins.<ref>PMID:10198056</ref> <ref>PMID:11387200</ref> <ref>PMID:11694577</ref> <ref>PMID:15692566</ref>

== Publication Abstract from PubMed ==

Ceramide synthases (CerS) catalyze ceramide formation via N-acylation of a sphingoid base with a fatty acyl-CoA and are attractive drug targets for treating numerous metabolic diseases and cancers. Here, we present the cryo-EM structure of a yeast CerS complex, consisting of a catalytic Lac1 subunit and a regulatory Lip1 subunit, in complex with C26-CoA substrate. The CerS holoenzyme exists as a dimer of Lac1-Lip1 heterodimers. Lac1 contains a hydrophilic reaction chamber and a hydrophobic tunnel for binding the CoA moiety and C26-acyl chain of C26-CoA, respectively. Lip1 interacts with both the transmembrane region and the last luminal loop of Lac1 to maintain the proper acyl chain binding tunnel. A lateral opening on Lac1 serves as a potential entrance for the sphingoid base substrate. Our findings provide a template for understanding the working mechanism of eukaryotic ceramide synthases and may facilitate the development of therapeutic CerS modulators.

~~Authors~~:

Structure and mechanism of a eukaryotic ceramide synthase complex.,Xie T, Fang Q, Zhang Z, Wang Y, Dong F, Gong X EMBO J. 2023 Dec 11;42(24):e114889. doi: 10.15252/embj.2023114889. Epub 2023 Nov , 13. PMID:37953642<ref>PMID:37953642</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Saccharomyces cerevisiae S288C]]

[[Category: Fang Q]]

[[Category: Gong X]]

[[Category: Xie T]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8izf is ON HOLD  until 2025-04-07
+==Cryo-EM structure of the Lac1-Lip1 (Lip1-S74F) complex==
+<StructureSection load='8izf' size='340' side='right'caption='[[8izf]], [[Resolution|resolution]] 3.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8izf]] is a 4 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=8IZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IZF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PL:(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM+4-OXIDE'>6PL</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=8izf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8izf OCA], [https://pdbe.org/8izf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8izf RCSB], [https://www.ebi.ac.uk/pdbsum/8izf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8izf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LAC1_YEAST LAC1_YEAST] Component of the ceramide synthase complex that catalyzes the transfer of the acyl chain from acyl-CoA to a sphingoid base, with high selectivity toward hexacosanoyl-CoA (C26:0-CoA) (PubMed:15692566, PubMed:11694577). N-acylates sphinganine and phytosphingosine bases to form dihydroceramides and phytoceramides, respectively (PubMed:15692566, PubMed:11694577). Redundant with LAG1. Facilitates ER-to-Golgi transport of GPI-anchored proteins.<ref>PMID:10198056</ref> <ref>PMID:11387200</ref> <ref>PMID:11694577</ref> <ref>PMID:15692566</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ceramide synthases (CerS) catalyze ceramide formation via N-acylation of a sphingoid base with a fatty acyl-CoA and are attractive drug targets for treating numerous metabolic diseases and cancers. Here, we present the cryo-EM structure of a yeast CerS complex, consisting of a catalytic Lac1 subunit and a regulatory Lip1 subunit, in complex with C26-CoA substrate. The CerS holoenzyme exists as a dimer of Lac1-Lip1 heterodimers. Lac1 contains a hydrophilic reaction chamber and a hydrophobic tunnel for binding the CoA moiety and C26-acyl chain of C26-CoA, respectively. Lip1 interacts with both the transmembrane region and the last luminal loop of Lac1 to maintain the proper acyl chain binding tunnel. A lateral opening on Lac1 serves as a potential entrance for the sphingoid base substrate. Our findings provide a template for understanding the working mechanism of eukaryotic ceramide synthases and may facilitate the development of therapeutic CerS modulators.
-Authors:
+Structure and mechanism of a eukaryotic ceramide synthase complex.,Xie T, Fang Q, Zhang Z, Wang Y, Dong F, Gong X EMBO J. 2023 Dec 11;42(24):e114889. doi: 10.15252/embj.2023114889. Epub 2023 Nov , 13. PMID:37953642<ref>PMID:37953642</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8izf" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae S288C]]
+[[Category: Fang Q]]
+[[Category: Gong X]]
+[[Category: Xie T]]