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Yorodumi- PDB-7wld: Cryo-EM structure of the human glycosylphosphatidylinositol trans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wld | ||||||||||||||||||
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Title | Cryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53 Angstrom resolution | ||||||||||||||||||
Components |
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Keywords | TRANSFERASE / GPI anchoring / GPI-AP / glycosylphosphatidylinositol transamidase / GPI transamidase / membrane protein complex | ||||||||||||||||||
Function / homology | Function and homology information 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 / Hydrolases / regulation of receptor signaling pathway via JAK-STAT / protein disulfide isomerase activity / tubulin binding ...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 / Hydrolases / regulation of receptor signaling pathway via JAK-STAT / protein disulfide isomerase activity / tubulin binding / neuron differentiation / cytoplasmic vesicle / protein-containing complex assembly / neuron apoptotic process / centrosome / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / proteolysis / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å | ||||||||||||||||||
Authors | Xu, Y. / Li, T. / Luo, Y. / Chao, Y. / Jia, G. / Zhou, Z. / Su, Z. / Qu, Q. / Li, D. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular insights into biogenesis of glycosylphosphatidylinositol anchor proteins. Authors: Yidan Xu / Guowen Jia / Tingting Li / Zixuan Zhou / Yitian Luo / Yulin Chao / Juan Bao / Zhaoming Su / Qianhui Qu / Dianfan Li / Abstract: Eukaryotic cells are coated with an abundance of glycosylphosphatidylinositol anchor proteins (GPI-APs) that play crucial roles in fertilization, neurogenesis, and immunity. The removal of a ...Eukaryotic cells are coated with an abundance of glycosylphosphatidylinositol anchor proteins (GPI-APs) that play crucial roles in fertilization, neurogenesis, and immunity. The removal of a hydrophobic signal peptide and covalent attachment of GPI at the new carboxyl terminus are catalyzed by an endoplasmic reticulum membrane GPI transamidase complex (GPI-T) conserved among all eukaryotes. Here, we report the cryo-electron microscopy (cryo-EM) structure of the human GPI-T at a global 2.53-Å resolution, revealing an equimolar heteropentameric assembly. Structure-based mutagenesis suggests a legumain-like mechanism for the recognition and cleavage of proprotein substrates, and an endogenous GPI in the structure defines a composite cavity for the lipid substrate. This elongated active site, stemming from the membrane and spanning an additional ~22-Å space toward the catalytic dyad, is structurally suited for both substrates which feature an amphipathic pattern that matches this geometry. Our work presents an important step towards the mechanistic understanding of GPI-AP biosynthesis. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wld.cif.gz | 487.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wld.ent.gz | 385.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/7wld ftp://data.pdbj.org/pub/pdb/validation_reports/wl/7wld | HTTPS FTP |
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-Related structure data
Related structure data | 32582MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules GKU
#1: Protein | Mass: 96990.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPAA1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O43292 |
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#2: Protein | Mass: 73443.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIGK / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q92643, Hydrolases |
#5: Protein | Mass: 80691.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIGU / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9H490 |
-GPI transamidase component PIG- ... , 2 types, 2 molecules ST
#3: Protein | Mass: 90421.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIGS / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q96S52 |
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#4: Protein | Mass: 94207.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIGT / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q969N2 |
-Sugars , 3 types, 4 molecules
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
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#13: Sugar | #16: Sugar | ChemComp-PA1 / | |
-Non-polymers , 11 types, 24 molecules
#7: Chemical | ChemComp-Y01 / #8: Chemical | ChemComp-AJP / | #9: Chemical | #10: Chemical | ChemComp-PEE / | #11: Chemical | ChemComp-CA / | #12: Chemical | ChemComp-P5S / | #14: Chemical | ChemComp-CLR / #15: Chemical | ChemComp-05E / | #17: Chemical | ChemComp-CDL / | #18: Chemical | ChemComp-DKB / [( | #19: Chemical | ChemComp-06O / [( | |
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-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 |
-Sample preparation
Component | Name: GPI transamidase complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 20 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 % |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2959791 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151590 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||
Refinement | Highest resolution: 2.53 Å | ||||||||||||||||||||||||||||
Refine LS restraints |
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