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Yorodumi- PDB-5h9o: Complex of Murine endoplasmic reticulum alpha-glucosidase II with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h9o | ||||||
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Title | Complex of Murine endoplasmic reticulum alpha-glucosidase II with D-Glucose | ||||||
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: 2.37 Å | ||||||
Authors | Caputo, A.T. / Roversi, P. / Alonzi, D.S. / Kiappes, J.L. / Zitzmann, N. | ||||||
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 | 5h9o.cif.gz | 725.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h9o.ent.gz | 611.8 KB | Display | PDB format |
PDBx/mmJSON format | 5h9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/5h9o ftp://data.pdbj.org/pub/pdb/validation_reports/h9/5h9o | HTTPS FTP |
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-Related structure data
Related structure data | 5f0eC 5hjoC 5hjrC 5iedC 5ieeC 5iefC 5iegC 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 97894.625 Da / Num. of mol.: 2 / Fragment: UNP Residues 33-944 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 #2: Protein | Mass: 9568.298 Da / Num. of mol.: 2 / Fragment: UNP residues 30-117 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 |
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-Sugars , 2 types, 6 molecules
#3: Sugar | ChemComp-NAG / #9: Sugar | |
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-Non-polymers , 8 types, 476 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-FMT / #6: Chemical | ChemComp-PG4 / #7: Chemical | ChemComp-P6G / #8: Chemical | ChemComp-OXM / | #10: Chemical | ChemComp-CA / #11: Chemical | ChemComp-TAR / | #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: 2.3 Å3/Da / Density % sol: 46.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: 32 % Morpheus ethylene glycol/PEG 8000 mix, 0.05 M Morpheus carboxylic acids mix, 0.1 M Morpheus buffer system 1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→87.88 Å / Num. obs: 89708 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 33.37 Å2 / Rsym value: 0.24 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.37→2.43 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 6578 / Rsym value: 1.53 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→87.66 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.882 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.414 / SU Rfree Blow DPI: 0.25
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Displacement parameters | Biso mean: 33.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→87.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.37→2.43 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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