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- PDB-2nt0: Acid-beta-glucosidase low pH, glycerol bound -

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Basic information

Entry
Database: PDB / ID: 2nt0
TitleAcid-beta-glucosidase low pH, glycerol bound
ComponentsGlucosylceramidase
KeywordsHYDROLASE / cerezyme / glucocerebrosidase / glucosylceramide / hydrolysis / gaucher disease
Function / homology
Function and homology information


steryl-beta-glucosidase activity / positive regulation of neuronal action potential / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / scavenger receptor binding / positive regulation of protein lipidation ...steryl-beta-glucosidase activity / positive regulation of neuronal action potential / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / scavenger receptor binding / positive regulation of protein lipidation / lymphocyte migration / glucosylceramide catabolic process / regulation of lysosomal protein catabolic process / glucosylceramidase activity / sphingosine biosynthetic process / autophagosome organization / microglial cell proliferation / glucosyltransferase activity / regulation of TOR signaling / response to thyroid hormone / Glycosphingolipid catabolism / microglia differentiation / ceramide biosynthetic process / positive regulation of type 2 mitophagy / lipid storage / lipid glycosylation / brain morphogenesis / positive regulation of protein-containing complex disassembly / response to pH / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / pyramidal neuron differentiation / negative regulation of protein metabolic process / motor behavior / lysosome organization / Transferases; Glycosyltransferases; Hexosyltransferases / neuromuscular process / hematopoietic stem cell proliferation / antigen processing and presentation / Association of TriC/CCT with target proteins during biosynthesis / response to testosterone / response to dexamethasone / negative regulation of interleukin-6 production / homeostasis of number of cells / regulation of macroautophagy / establishment of skin barrier / negative regulation of MAPK cascade / negative regulation of protein-containing complex assembly / cell maturation / mitophagy / cholesterol metabolic process / lysosomal lumen / cellular response to starvation / respiratory electron transport chain / 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 / neuron apoptotic process / negative regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosome / signaling receptor binding / lysosomal membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsLieberman, R.L. / Petsko, G.A. / Ringe, D.
Citation
Journal: Nat.Chem.Biol. / Year: 2007
Title: Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease.
Authors: Lieberman, R.L. / Wustman, B.A. / Huertas, P. / Powe, A.C. / Pine, C.W. / Khanna, R. / Schlossmacher, M.G. / Ringe, D. / Petsko, G.A.
#1: Journal: Nat.Chem.Biol. / Year: 2006
Title: Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease
History
DepositionNov 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification ..._pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosylceramidase
B: Glucosylceramidase
C: Glucosylceramidase
D: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,78542
Polymers222,5614
Non-polymers4,22538
Water30,8061710
1
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4308
Polymers55,6401
Non-polymers7907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,93512
Polymers55,6401
Non-polymers1,29511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,61010
Polymers55,6401
Non-polymers9709
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,81012
Polymers55,6401
Non-polymers1,17011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.941, 91.759, 152.810
Angle α, β, γ (deg.)90.00, 110.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glucosylceramidase / Beta-glucocerebrosidase / Acid beta-glucosidase / D-glucosyl-N-acylsphingosine glucohydrolase / ...Beta-glucocerebrosidase / Acid beta-glucosidase / D-glucosyl-N-acylsphingosine glucohydrolase / Alglucerase / Imiglucerase


Mass: 55640.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P04062, glucosylceramidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1710 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1 M Ammonium Sulfate 0.17 M Guanidinium HCl 0.02 M KCl 0.1 M Acetate buffer pH 4.5 Cryoprotectant includes 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 220956 / % possible obs: 84.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 24.35 Å2 / Rsym value: 0.062 / Χ2: 1.025 / Net I/σ(I): 7.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 18569 / Rsym value: 0.417 / Χ2: 0.622 / % possible all: 71.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGS monomer

1ogs


Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.437 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 11117 5 %RANDOM
Rwork0.179 ---
obs0.181 220955 84.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.352 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å2-0.33 Å2
2---1.24 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15720 0 248 1710 17678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02216525
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.95822584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83351984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93123.444720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.367152516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4131584
X-RAY DIFFRACTIONr_chiral_restr0.1150.22416
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212536
X-RAY DIFFRACTIONr_nbd_refined0.2190.28643
X-RAY DIFFRACTIONr_nbtor_refined0.3080.211086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.21673
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.226
X-RAY DIFFRACTIONr_mcbond_it1.0111.510191
X-RAY DIFFRACTIONr_mcangle_it1.53216072
X-RAY DIFFRACTIONr_scbond_it2.48537184
X-RAY DIFFRACTIONr_scangle_it3.6224.56328
LS refinement shellResolution: 1.788→1.835 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 588 -
Rwork0.269 11696 -
obs-12284 63.17 %

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