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Yorodumi- PDB-6ytr: Structure of recombinant human beta-glucocerebrosidase in complex... -
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-Basic information
Entry | Database: PDB / ID: 6ytr | ||||||
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Title | Structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol aziridine inhibitor | ||||||
Components | Lysosomal acid glucosylceramidase | ||||||
Keywords | HYDROLASE / beta-glucocerebrosidase / lysosomal glycoside hydrolase / GH30 / Cyclophellitol aziridine / Inhibitor / Complex | ||||||
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 / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / 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 / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / lymphocyte migration / glucosylceramidase / glucosylceramide catabolic process / scavenger receptor binding / regulation of lysosomal protein catabolic process / autophagosome organization / sphingosine biosynthetic process / glucosylceramidase activity / microglial cell proliferation / glucosyltransferase activity / regulation of TOR signaling / 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 / antigen processing and presentation / homeostasis of number of cells / 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 / cellular response to tumor necrosis factor / T cell differentiation in thymus / 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: 1.7 Å | ||||||
Authors | Rowland, R.J. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chemistry / Year: 2021 Title: Design, Synthesis and Structural Analysis of Glucocerebrosidase Imaging Agents. Authors: Rowland, R.J. / Chen, Y. / Breen, I. / Wu, L. / Offen, W.A. / Beenakker, T.J. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Aerts, J.M.F.G. / Artola, M. / Overkleeft, H.S. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ytr.cif.gz | 430.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ytr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ytr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/6ytr ftp://data.pdbj.org/pub/pdb/validation_reports/yt/6ytr | HTTPS FTP |
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-Related structure data
Related structure data | 6ytpC 6yutC 6yv3C 6z39C 6z3iC 2nt0S 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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-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 55659.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Recombinant human beta-glucocerebrosidase missing its 40-amino acid signalling sequence Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC, GLUC / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P04062, glucosylceramidase, Transferases; Glycosyltransferases; Hexosyltransferases, steryl-beta-glucosidase |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 930 molecules
#5: Chemical | #6: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-EDO / #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.07 Å3/Da / Density % sol: 59.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→66.799 Å / Num. obs: 119361 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.064 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 1.83 / Mean I/σ(I) obs: 1 / Num. unique obs: 5867 / CC1/2: 0.547 / Rpim(I) all: 1.07 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NT0 Resolution: 1.7→66.799 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.163 / SU B: 2.808 / SU ML: 0.086 / Average fsc free: 0.8881 / Average fsc work: 0.9009 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.1 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.919 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→66.799 Å
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Refine LS restraints |
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LS refinement shell |
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