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- PDB-1y7v: X-ray structure of human acid-beta-glucosidase covalently bound t... -

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Basic information

Entry
Database: PDB / ID: 1y7v
TitleX-ray structure of human acid-beta-glucosidase covalently bound to conduritol B epoxide
ComponentsGlucosylceramidase
KeywordsHYDROLASE / GAUCHER DISEASE / GLUCOSIDASE / GLUCOCEREBROSIDASE / CEREZYME / GLYCOSIDASE / SPHINGOLIPID METABOLISM / GLYCOPROTEIN / LYSOSOME / MEMBRANE / DISEASE MUTATION / ALTERNATIVE INITIATION / Israel Structural Proteomics Center / ISPC / Structural Genomics
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 / response to pH / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 / cholesterol metabolic process / respiratory electron transport chain / cellular response to starvation / lysosomal lumen / negative regulation of MAP kinase activity / determination of adult lifespan / trans-Golgi network / negative regulation of inflammatory response / autophagy / 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
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
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Difference Fourier technique / Resolution: 2.4 Å
AuthorsPremkumar, L. / Sawkar, A.R. / Boldin-Adamsky, S. / Toker, L. / Silman, I. / Kelly, J.W. / Futerman, A.H. / Sussman, J.L. / Israel Structural Proteomics Center (ISPC)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: X-ray structure of human acid-beta-glucosidase covalently bound to conduritol-B-epoxide. Implications for Gaucher disease.
Authors: Premkumar, L. / Sawkar, A.R. / Boldin-Adamsky, S. / Toker, L. / Silman, I. / Kelly, J.W. / Futerman, A.H. / Sussman, J.L.
History
DepositionDec 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosylceramidase
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,73819
Polymers111,2802
Non-polymers2,45817
Water5,152286
1
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,91710
Polymers55,6401
Non-polymers1,2779
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8219
Polymers55,6401
Non-polymers1,1818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Glucosylceramidase
hetero molecules

A: Glucosylceramidase
hetero molecules

B: Glucosylceramidase
hetero molecules

B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,47738
Polymers222,5614
Non-polymers4,91634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area13550 Å2
ΔGint-354 kcal/mol
Surface area68140 Å2
MethodPISA
4
A: Glucosylceramidase
hetero molecules

A: Glucosylceramidase
hetero molecules

B: Glucosylceramidase
hetero molecules

B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,47738
Polymers222,5614
Non-polymers4,91634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area15580 Å2
ΔGint-350 kcal/mol
Surface area66110 Å2
MethodPISA
5
A: Glucosylceramidase
hetero molecules

B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,73819
Polymers111,2802
Non-polymers2,45817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area5640 Å2
ΔGint-166 kcal/mol
Surface area35200 Å2
MethodPISA
6
A: Glucosylceramidase
hetero molecules

A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,83420
Polymers111,2802
Non-polymers2,55418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5000 Å2
ΔGint-130 kcal/mol
Surface area35500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.49, 285.61, 91.51
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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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.: 2 / Mutation: R495H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC / Cell line (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P04062, glucosylceramidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL / Inositol


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Comment: neurotransmitter, hormone*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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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: 3.071 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Ammonium sulfate, guanidine HCl, KCl, acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 55602 / Num. obs: 55401 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 12.75
Reflection shellResolution: 2.4→2.5 Å / Mean I/σ(I) obs: 4.88 / % possible all: 95.7

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
CNSrefinement
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: Difference Fourier technique
Starting model: PDB entry 1OGS

1ogs


Resolution: 2.4→28.82 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2686 -Random
Rwork0.242 ---
all0.244 53193 --
obs0.244 53193 98.6 %-
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-28.23 Å20 Å20 Å2
2---9.87 Å20 Å2
3----18.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7860 0 143 286 8289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.1

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