+Open data
-Basic information
Entry | Database: PDB / ID: 5f0e | |||||||||
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Title | Murine endoplasmic reticulum alpha-glucosidase II | |||||||||
Components |
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Keywords | HYDROLASE / Enzyme Glycosyl hydrolase GH31 Quality control exoglycosidase | |||||||||
Function / homology | Function and homology information mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / alpha-glucosidase activity / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / alpha-glucosidase activity / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development / carbohydrate binding / in utero embryonic development / carbohydrate metabolic process / intracellular membrane-bounded organelle / calcium ion binding / protein-containing complex binding / Golgi apparatus / endoplasmic reticulum / RNA binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | |||||||||
Authors | Caputo, A.T. / Roversi, P. / Alonzi, D.S. / Kiappes, J.L. / Zitzmann, N. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structures of mammalian ER alpha-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals. Authors: Caputo, A.T. / Alonzi, D.S. / Marti, L. / Reca, I.B. / Kiappes, J.L. / Struwe, W.B. / Cross, A. / Basu, S. / Lowe, E.D. / Darlot, B. / Santino, A. / Roversi, P. / Zitzmann, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f0e.cif.gz | 398.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f0e.ent.gz | 321.7 KB | Display | PDB format |
PDBx/mmJSON format | 5f0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f0e ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f0e | HTTPS FTP |
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-Related structure data
Related structure data | 5h9oC 5hjoC 5hjrC 5iedC 5ieeC 5iefC 5iegC 3l4zS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 97894.625 Da / Num. of mol.: 1 / Fragment: UNP Residues 33-966 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q8BHN3, EC: 3.2.1.84 |
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#2: Protein | Mass: 9568.298 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Plasmid: pHLsec / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: O08795 |
-Sugars , 1 types, 1 molecules
#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 |
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-Non-polymers , 6 types, 944 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FMT / #8: Chemical | #9: 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: 2.59 Å3/Da / Density % sol: 52.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 32% Morpheus ethylene glycol/PEG 8000 mix, 0.05 M Morpheus carbxylic acid mix, 0.1 M Morpheus buffer system 1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96597 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96597 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→59.09 Å / Num. obs: 109959 / % possible obs: 94.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.32 Å2 / Rsym value: 0.077 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.663 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L4Z Resolution: 1.74→59.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.091 / SU Rfree Blow DPI: 0.087 / SU Rfree Cruickshank DPI: 0.085
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Displacement parameters | Biso mean: 23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→59.09 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.74 Å / Rfactor Rfree error: 0
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