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- PDB-8imy: Cryo-EM structure of GPI-T (inactive mutant) with GPI and proULBP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8imy | ||||||
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Title | Cryo-EM structure of GPI-T (inactive mutant) with GPI and proULBP2, a proprotein substrate | ||||||
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![]() | MEMBRANE PROTEIN / cryo-EM / glycosylphosphatidylinositol / GPI / GPI anchored protein / GPI-AP / membrane protein complex / proprotein | ||||||
Function / homology | ![]() GPI-anchor transamidase activity / attachment of GPI anchor to protein / GPI-anchor transamidase complex / GPI anchor biosynthetic process / protein retention in ER lumen / Attachment of GPI anchor to uPAR / natural killer cell lectin-like receptor binding / Post-translational modification: synthesis of GPI-anchored proteins / Hydrolases / natural killer cell mediated cytotoxicity ...GPI-anchor transamidase activity / attachment of GPI anchor to protein / GPI-anchor transamidase complex / GPI anchor biosynthetic process / protein retention in ER lumen / Attachment of GPI anchor to uPAR / natural killer cell lectin-like receptor binding / Post-translational modification: synthesis of GPI-anchored proteins / Hydrolases / natural killer cell mediated cytotoxicity / natural killer cell activation / regulation of receptor signaling pathway via JAK-STAT / protein disulfide isomerase activity / tubulin binding / bioluminescence / generation of precursor metabolites and energy / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / neuron differentiation / positive regulation of T cell mediated cytotoxicity / cytoplasmic vesicle / protein-containing complex assembly / neuron apoptotic process / immune response / external side of plasma membrane / intracellular membrane-bounded organelle / centrosome / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / mitochondrion / proteolysis / extracellular space / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å | ||||||
![]() | Li, T. / Xu, Y. / Qu, Q. / Li, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis. Authors: Yidan Xu / Tingting Li / Zixuan Zhou / Jingjing Hong / Yulin Chao / Zhini Zhu / Ying Zhang / Qianhui Qu / Dianfan Li / ![]() Abstract: 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 ...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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 509.6 KB | Display | ![]() |
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PDB format | ![]() | 380.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 93.5 KB | Display | |
Data in CIF | ![]() | 129.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35576MC ![]() 8imxC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 4 molecules GKUD
#1: Protein | Mass: 96990.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GPAA1, GAA1 / Production host: ![]() |
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#2: Protein | Mass: 73426.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PIGK, GPI8 / Production host: ![]() |
#3: Protein | Mass: 80691.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PIGU, CDC91L1, PSEC0205, UNQ3055/PRO9875 / Production host: ![]() |
#6: Protein | Mass: 28790.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-GPI transamidase component PIG- ... , 2 types, 2 molecules TS
#4: Protein | Mass: 92825.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PIGT, CGI-06, PSEC0163, UNQ716/PRO1379 / Production host: ![]() |
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#5: Protein | Mass: 90421.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PIGS, UNQ1873/PRO4316 / Production host: ![]() |
-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
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#7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#16: Sugar | #18: Sugar | ChemComp-PA1 / | |
-Non-polymers , 10 types, 34 molecules ![](data/chem/img/AJP.gif)
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![](data/chem/img/LBN.gif)
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#8: Chemical | ChemComp-AJP / | ||||||||||||||||
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#9: Chemical | ChemComp-6OU / [( #10: Chemical | ChemComp-Y01 / #11: Chemical | ChemComp-MG / | #12: Chemical | ChemComp-05E / | #13: Chemical | #14: Chemical | ChemComp-CA / | #15: Chemical | ChemComp-LBN / | #17: Chemical | ChemComp-81Q / [( | #19: Chemical | ChemComp-80T / [( | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Complex of GPI-T (inactive mutant) with GPI and proULBP2 Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 463 kDa/nm / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||
Buffer solution | pH: 8 Details: 0.1 % Digitonin, 150 mM NaCl, 20 mM Tris-HCl pH 8.0 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 53648 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4555 |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: The images were high-pass filtered and normalized | ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2981565 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176889 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refine LS restraints |
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