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- EMDB-36996: Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Ch... -
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Open data
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Basic information
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Title | Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum | |||||||||
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![]() | Bst1 / Glycosylphosphatidylinositol / GPI anchoring / GPI-AP / GPI-AP remodelase / Integral membrane enzyme / Lipase / Lipid remodeling / Membrane enzyme / Membrane protein / Nanodisc / PGAP1 / TGP / Thermostable green fluorescence protein / Transmembrane enzyme / Triad enzyme. | |||||||||
Function / homology | ![]() GPI anchor metabolic process / phosphatidylinositol deacylase activity / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation ...GPI anchor metabolic process / phosphatidylinositol deacylase activity / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / side of membrane / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / bioluminescence / secretory granule membrane / generation of precursor metabolites and energy / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of T cell cytokine production / protein transport / virus receptor activity / positive regulation of cytosolic calcium ion concentration / Hydrolases; Acting on ester bonds / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / endoplasmic reticulum membrane / cell surface / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.68 Å | |||||||||
![]() | Li T / Hong J / Qu Q / Li D | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis. Authors: Jingjing Hong / Tingting Li / Yulin Chao / Yidan Xu / Zhini Zhu / Zixuan Zhou / Weijie Gu / Qianhui Qu / Dianfan Li / ![]() Abstract: The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates ...The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates the inositol in nascent GPI-APs. Impairment of PGAP1 activity leads to developmental diseases in humans and fatality and infertility in animals. Here, we present three PGAP1 structures (2.66-2.84 Å), revealing its 10-transmembrane architecture and product-enzyme interaction details. PGAP1 holds GPI-AP acyl chains in an optimally organized, guitar-shaped cavity with apparent energetic penalties from hydrophobic-hydrophilic mismatches. However, abundant glycan-mediated interactions in the lumen counterbalance these repulsions, likely conferring substrate fidelity and preventing off-target hydrolysis of bulk membrane lipids. Structural and biochemical analyses uncover a serine hydrolase-type catalysis with atypical features and imply mechanisms for substrate entrance and product release involving a drawing compass movement of GPI-APs. Our findings advance the mechanistic understanding of GPI-AP remodeling. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 70.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.7 KB 23.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 79.5 KB | ||
Filedesc metadata | ![]() | 8.1 KB | ||
Others | ![]() ![]() ![]() | 37.9 MB 69.8 MB 69.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k9rMC ![]() 8k9qC ![]() 8k9tC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
File | emd_36996_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Complex of the GPI inositol-deacylase with a chimera GPI-anchored...
+Supramolecule #1: Complex of the GPI inositol-deacylase with a chimera GPI-anchored...
+Macromolecule #1: GPI inositol-deacylase,MCherry protein
+Macromolecule #2: Green fluorescent protein,Complement decay-accelerating factor
+Macromolecule #3: alpha-D-mannopyranose
+Macromolecule #4: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-...
+Macromolecule #5: 2-amino-2-deoxy-alpha-D-glucopyranose
+Macromolecule #6: [(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,...
+Macromolecule #7: PALMITIC ACID
+Macromolecule #8: CHOLESTEROL
+Macromolecule #9: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-...
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |