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Yorodumi- PDB-5iee: Murine endoplasmic reticulum alpha-glucosidase II with 1-deoxynoj... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iee | |||||||||
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Title | Murine endoplasmic reticulum alpha-glucosidase II with 1-deoxynojirimycin | |||||||||
Components |
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Keywords | HYDROLASE / Enzyme Glycosyl hydrolase GH31 Quality control exoglycosidase / DNJ | |||||||||
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 / : / protein kinase C binding ...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 / : / protein kinase C binding / liver development / phosphoprotein binding / melanosome / negative regulation of neuron projection development / carbohydrate binding / in utero embryonic development / transmembrane transporter binding / 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 / FOURIER SYNTHESIS / Resolution: 1.92 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 | 5iee.cif.gz | 404.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iee.ent.gz | 325.7 KB | Display | PDB format |
PDBx/mmJSON format | 5iee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/5iee ftp://data.pdbj.org/pub/pdb/validation_reports/ie/5iee | HTTPS FTP |
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-Related structure data
Related structure data | 5f0eSC 5h9oC 5hjoC 5hjrC 5iedC 5iefC 5iegC 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 106157.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-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 Details: This chain contains all of the residues from the mature O08795 but has been trypsinised so that there all that was crystallised are residues: 30-117 Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Plasmid: pOPING / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / 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 , 7 types, 976 molecules
#4: Chemical | Mass: 194.226 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Formula: C8H18O5 Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) Mus musculus (house mouse) / Gene: ganab / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: EC: 3.2.1.84 / Comment: precipitant*YM #5: Chemical | ChemComp-P6G / Mass: 282.331 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C12H26O7 Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) Mus musculus (house mouse) / Gene: ganab / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: EC: 3.2.1.84 / Comment: precipitant*YM #6: Chemical | ChemComp-EDO / Mass: 62.068 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Formula: C2H6O2 Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) Mus musculus (house mouse) / Gene: ganab / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: EC: 3.2.1.84 #7: Chemical | ChemComp-FMT / Mass: 46.025 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Formula: CH2O2 Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive) Source: (gene. exp.) Mus musculus (house mouse) / Gene: ganab / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: EC: 3.2.1.84 #8: Chemical | ChemComp-NOJ / | #9: Chemical | #10: 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: 2.57 Å3/Da / Density % sol: 52.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 21% v/v ethylene glycol, 11% w/v PEG 8000 (from the Morpheus Precipitant Mix 2), 50 mM Morpheus carboxylic acids mix, 100 mM Morpheus buffer system 1 pH 6.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.919→88.901 Å / Num. obs: 87597 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.34 Å2 / Rsym value: 0.239 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.919→1.925 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5F0E Resolution: 1.92→88.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.119
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Displacement parameters | Biso mean: 28.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.92→88.9 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.92 Å / Rfactor Rfree error: 0
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