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- PDB-8k9q: Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k9q | ||||||
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Title | Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from Chaetomium thermophilum | ||||||
![]() | GPI inositol-deacylase,fused thermostable green fluorescent protein | ||||||
![]() | MEMBRANE PROTEIN / Bst1 / Glycosylphosphatidylinositol / GPI anchoring / GPI-AP / GPI-AP remodelase / Integral membrane enzyme / Lipase / Lipid remodeling / Membrane enzyme / Nanodisc / PGAP1 / Transmembrane enzyme / Triad enzyme | ||||||
Function / homology | ![]() GPI anchor metabolic process / phosphatidylinositol deacylase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / Hydrolases; Acting on ester bonds / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||
![]() | Hong, J. / Li, T. / 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 192.4 KB | Display | ![]() |
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PDB format | ![]() | 142.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 635.2 KB | Display | ![]() |
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Full document | ![]() | 658.9 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 36995MC ![]() 8k9rC ![]() 8k9tC 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
#1: Protein | Mass: 163153.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The protein is a fusion protein with expression tag. Residues 1187-1196 is the linker with a 3 C protease digestion site. Residues 1197-1427 is a fused thermostable green fluorescent protein ...Details: The protein is a fusion protein with expression tag. Residues 1187-1196 is the linker with a 3 C protease digestion site. Residues 1197-1427 is a fused thermostable green fluorescent protein (PDB entry 4TZA, residue 5-229). Residues 1428-1469 is the linker a Strep II tag and a His tag. Source: (gene. exp.) ![]() Gene: CTHT_0034210 / Production host: ![]() References: UniProt: G0S652, Hydrolases; Acting on ester bonds | ||||
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#2: Chemical | #3: Chemical | Has ligand of interest | N | |
-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: GPI inositol-deacylase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.163 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 7.5 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: 277.15 K / Details: Blot for 4.5s before plunging |
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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 defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 407921 / Symmetry type: POINT | ||||||||||||||||||||||||||||
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