+Open data
-Basic information
Entry | Database: PDB / ID: 2v3e | |||||||||
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Title | acid-beta-glucosidase with N-nonyl-deoxynojirimycin | |||||||||
Components | GLUCOSYLCERAMIDASE | |||||||||
Keywords | HYDROLASE / ACID-BETA-GLUCOSIDASE / N-NONYL-DEOXYNOJIRIMYCINALTERNATIVE INITIATION / SPHINGOLIPID METABOLISM / N-NONYL-DEOXYNOJIRIMYCIN / GAUCHER DISEASE / DISEASE MUTATION / LIPID METABOLISM / POLYMORPHISM / GLYCOPROTEIN / PHARMACEUTICAL / ALTERNATIVE SPLICING / MEMBRANE / LYSOSOME / GLYCOSIDASE | |||||||||
Function / homology | Function and homology information positive regulation of protein lipidation / steryl-beta-glucosidase activity / beta-glucoside catabolic process / positive regulation of neuronal action potential / cerebellar Purkinje cell layer formation / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / lymphocyte migration ...positive regulation of protein lipidation / steryl-beta-glucosidase activity / beta-glucoside catabolic process / positive regulation of neuronal action potential / cerebellar Purkinje cell layer formation / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / lymphocyte migration / glucosylceramidase / glucosylceramide catabolic process / scavenger receptor binding / regulation of lysosomal protein catabolic process / sphingosine biosynthetic process / autophagosome organization / glucosylceramidase activity / microglial cell proliferation / regulation of TOR signaling / glucosyltransferase activity / ceramide biosynthetic process / lipid storage / response to thyroid hormone / microglia differentiation / Glycosphingolipid catabolism / pyramidal neuron differentiation / lipid glycosylation / brain morphogenesis / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / response to pH / positive regulation of protein-containing complex disassembly / motor behavior / neuromuscular process / Transferases; Glycosyltransferases; Hexosyltransferases / hematopoietic stem cell proliferation / lysosome organization / response to testosterone / response to dexamethasone / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of interleukin-6 production / homeostasis of number of cells / antigen processing and presentation / regulation of macroautophagy / establishment of skin barrier / negative regulation of protein-containing complex assembly / positive regulation of protein dephosphorylation / cell maturation / respiratory electron transport chain / cellular response to starvation / cholesterol metabolic process / lysosomal lumen / negative regulation of MAP kinase activity / determination of adult lifespan / trans-Golgi network / autophagy / negative regulation of inflammatory response / response to estrogen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / T cell differentiation in thymus / cellular response to tumor necrosis factor / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / negative regulation of neuron apoptotic process / lysosome / lysosomal membrane / signaling receptor binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Brumshtein, B. / Greenblatt, H.M. / Butters, T.D. / Shaaltiel, Y. / Aviezer, D. / Silman, I. / Futerman, A.H. / Sussman, J.L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structures of Complexes of N-Butyl- and N-Nonyl-Deoxynojirimycin Bound to Acid Beta-Glucosidase: Insights Into the Mechanism of Chemical Chaperone Action in Gaucher Disease. Authors: Brumshtein, B. / Greenblatt, H.M. / Butters, T.D. / Shaaltiel, Y. / Aviezer, D. / Silman, I. / Futerman, A.H. / Sussman, J.L. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" AND "BC" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" AND "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v3e.cif.gz | 231.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v3e.ent.gz | 184.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/2v3e ftp://data.pdbj.org/pub/pdb/validation_reports/v3/2v3e | HTTPS FTP |
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-Related structure data
Related structure data | 2v3dC 2v3fS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56589.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NN-DNJ IN THE ACTIVE SITE / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: DAUCUS CAROTA (carrot) / References: UniProt: P04062, glucosylceramidase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 1008 molecules
#3: Chemical | #4: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | IN ADDITION TO THE NATIVE SEQUENCE OF HUMAN ACID-BETA-GLUCOSIDASE, THE MOLECULE HAS 2 AMINO ACIDS ...IN ADDITION TO THE NATIVE SEQUENCE OF HUMAN ACID-BETA-GLUCOSIDAS |
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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: 47 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M NH4COOCH3, 0.1 M HEPES PH 7.5, 25% (W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.62 Å / Num. obs: 59655 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.27 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / % possible all: 52.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V3F Resolution: 2→23.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.927 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2→23.62 Å
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Refine LS restraints |
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