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Yorodumi- PDB-5nn8: Crystal structure of human lysosomal acid-alpha-glucosidase, GAA,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nn8 | |||||||||
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Title | Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with acarbose | |||||||||
Components | Lysosomal alpha-glucosidase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase / lysosome / glycogen catabolism / Pompe disease | |||||||||
Function / homology | Function and homology information vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-1,4-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / alpha-glucosidase activity / alpha-glucosidase / glycophagy / diaphragm contraction ...vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-1,4-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / alpha-glucosidase activity / alpha-glucosidase / glycophagy / 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: 2.45 Å | |||||||||
Authors | Roig-Zamboni, V. / Cobucci-Ponzano, B. / Iacono, R. / Ferrara, M.C. / Germany, S. / Parenti, G. / Bourne, Y. / Moracci, M. | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structure of human lysosomal acid alpha-glucosidase-a guide for the treatment of Pompe disease. Authors: Roig-Zamboni, V. / Cobucci-Ponzano, B. / Iacono, R. / Ferrara, M.C. / Germany, S. / Bourne, Y. / Parenti, G. / Moracci, M. / Sulzenbacher, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nn8.cif.gz | 354.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nn8.ent.gz | 284.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nn8_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5nn8_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 5nn8_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 5nn8_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/5nn8 ftp://data.pdbj.org/pub/pdb/validation_reports/nn/5nn8 | HTTPS FTP |
-Related structure data
Related structure data | 5nn3SC 5nn4C 5nn5C 5nn6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 A
#1: Protein | Mass: 96978.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Full-length rhGAA has been treated with alpha-chymotrypsin, leading to a sample starting at residue Gln81. Missing surface loops have equally been removed by proteolytic cleavage. Source: (gene. exp.) Homo sapiens (human) / Gene: GAA / Cell (production host): Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P10253, alpha-glucosidase |
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-Sugars , 5 types, 7 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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 #5: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose | #6: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / acarbose-derived trisaccharide | |
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-Non-polymers , 6 types, 313 molecules
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-EDO / #10: Chemical | ChemComp-GOL / | #11: Chemical | ChemComp-PGE / | #12: Water | ChemComp-HOH / | |
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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: 3.39 Å3/Da / Density % sol: 63.73 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→51.55 Å / Num. obs: 44773 / % possible obs: 94.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 25.97 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.116 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4760 / CC1/2: 0.644 / Rpim(I) all: 0.554 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5NN3 Resolution: 2.45→51.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.655 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.224 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.355 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→51.55 Å
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Refine LS restraints |
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