8imx
From Proteopedia
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<table><tr><td colspan='2'>[[8imx]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Clavularia_sp. Clavularia sp.], [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IMX FirstGlance]. <br> | <table><tr><td colspan='2'>[[8imx]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Clavularia_sp. Clavularia sp.], [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IMX 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]] 2.85Å</td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.85Å</td></tr> | ||
| - | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=05E:2-azanylethyl+[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]+hydrogen+phosphate'>05E</scene>, <scene name='pdbligand=6OU:[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl]+(~{Z})-octadec-9-enoate'>6OU</scene>, <scene name='pdbligand=80T:[( | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=05E:2-azanylethyl+[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]+hydrogen+phosphate'>05E</scene>, <scene name='pdbligand=6OU:[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl]+(~{Z})-octadec-9-enoate'>6OU</scene>, <scene name='pdbligand=80T:[(2~{R})-1-hexadecanoyloxy-3-[[3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl]+(~{Z})-octadec-9-enoate'>80T</scene>, <scene name='pdbligand=80Y:2-azanylethyl+[(2~{R},3~{S},4~{S},5~{S},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl+hydrogen+phosphate'>80Y</scene>, <scene name='pdbligand=81Q:[(2~{R})-1-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl]+(5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate'>81Q</scene>, <scene name='pdbligand=AJP:(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-2-[(2~{R},3~{R},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-4,5-bis(oxidanyl)-6-[(1~{R},2~{S},3~{S},4~{R},5~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{S},15~{R},16~{R},18~{S})-5,7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2-oxane]-16-yl]oxy-oxan-3-yl]oxy-5-oxidanyl-4-[(2~{S},3~{R},4~{S},5~{R})-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-oxan-3-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-oxane-3,4,5-triol'>AJP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LBN:(2R)-3-(hexadecanoyloxy)-2-{[(9Z)-octadec-9-enoyl]oxy}propyl+2-(trimethylazaniumyl)ethyl+phosphate'>LBN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PA1:2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE'>PA1</scene>, <scene name='pdbligand=Y01:CHOLESTEROL+HEMISUCCINATE'>Y01</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=8imx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8imx OCA], [https://pdbe.org/8imx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8imx RCSB], [https://www.ebi.ac.uk/pdbsum/8imx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8imx 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=8imx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8imx OCA], [https://pdbe.org/8imx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8imx RCSB], [https://www.ebi.ac.uk/pdbsum/8imx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8imx ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| - | == | + | <div style="background-color:#fffaf0;"> |
| - | + | == Publication Abstract from PubMed == | |
| + | Many eukaryotic receptors and enzymes rely on glycosylphosphatidylinositol (GPI) anchors for membrane localization and function. The transmembrane complex GPI-T recognizes diverse proproteins at a signal peptide region that lacks consensus sequence and replaces it with GPI via a transamidation reaction. How GPI-T maintains broad specificity while preventing unintentional cleavage is unclear. Here, substrates- and products-bound human GPI-T structures identify subsite features that enable broad proprotein specificity, inform catalytic mechanism, and reveal a multilevel safeguard mechanism against its promiscuity. In the absence of proproteins, the catalytic site is invaded by a locally stabilized loop. Activation requires energetically unfavorable rearrangements that transform the autoinhibitory loop into crucial catalytic cleft elements. Enzyme-proprotein binding in the transmembrane and luminal domains respectively powers the conformational rearrangement and induces a competent cleft. GPI-T thus integrates various weak specificity regions to form strong selectivity and prevent accidental activation. These findings provide important mechanistic insights into GPI-anchored protein biogenesis. | ||
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| + | Structures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis.,Xu Y, Li T, Zhou Z, Hong J, Chao Y, Zhu Z, Zhang Y, Qu Q, Li D Nat Commun. 2023 Sep 8;14(1):5520. doi: 10.1038/s41467-023-41281-y. PMID:37684232<ref>PMID:37684232</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 8imx" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
Cryo-EM structure of GPI-T with a chimeric GPI-anchored protein
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Categories: Clavularia sp | Homo sapiens | Large Structures | Synthetic construct | Li D | Li T | Qu Q | Xu Y
