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Yorodumi- PDB-7p32: Crystal structure of human lysosomal acid-alpha-glucosidase, GAA,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p32 | ||||||
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Title | Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 6 | ||||||
Components | Lysosomal alpha-glucosidase | ||||||
Keywords | HYDROLASE / alpha-glycosidase / lysosomal / Pompe disease / pharmacological chaperone | ||||||
Function / homology | Function and homology information vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / alpha-1,4-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / glycophagy / alpha-glucosidase / maltose alpha-glucosidase activity ...vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / alpha-1,4-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / glycophagy / alpha-glucosidase / maltose alpha-glucosidase activity / diaphragm contraction / neuromuscular process controlling posture / tissue development / regulation of the force of heart contraction / glycogen catabolic process / aorta development / azurophil granule membrane / Glycogen breakdown (glycogenolysis) / muscle cell cellular homeostasis / lysosome organization / tertiary granule membrane / neuromuscular process controlling balance / ficolin-1-rich granule membrane / heart morphogenesis / cardiac muscle contraction / lysosomal lumen / locomotory behavior / glucose metabolic process / carbohydrate binding / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.82 Å | ||||||
Authors | Roig-Zamboni, V. / Kok, K. / Overkleeft, H. / Artola, M. / Sulzenbacher, G. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: 1,6- epi-Cyclophellitol Cyclosulfamidate Is a Bona Fide Lysosomal alpha-Glucosidase Stabilizer for the Treatment of Pompe Disease. Authors: Kok, K. / Kuo, C.L. / Katzy, R.E. / Lelieveld, L.T. / Wu, L. / Roig-Zamboni, V. / van der Marel, G.A. / Codee, J.D.C. / Sulzenbacher, G. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.F.G. / Artola, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p32.cif.gz | 219.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p32.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/7p32 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/7p32 | HTTPS FTP |
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-Related structure data
Related structure data | 7p2zC 7p4cC 7p4dC 5nn4S C: citing same article (ref.) S: Starting model for refinement |
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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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 96978.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: sample is Myozyme / Source: (gene. exp.) Homo sapiens (human) / Gene: GAA / Cell line (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P10253, alpha-glucosidase |
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-Sugars , 5 types, 5 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: 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 |
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 703 molecules
#7: Chemical | ChemComp-56I / [( | ||||||||||
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#8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-CL / #10: Chemical | #11: Chemical | ChemComp-EDO / #12: Chemical | ChemComp-PGE / | #13: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.0, 2% V/V PEG400 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98009 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→47.68 Å / Num. obs: 115889 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Rrim(I) all: 0.108 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.82→1.85 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5464 / CC1/2: 0.492 / Rpim(I) all: 0.705 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5NN4 Resolution: 1.82→47 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.063 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.086 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.022 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→47 Å
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Refine LS restraints |
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LS refinement shell |
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