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- PDB-6z39: Structure of recombinant human beta-glucocerebrosidase in complex... -

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Basic information

Entry
Database: PDB / ID: 6z39
TitleStructure of recombinant human beta-glucocerebrosidase in complex with BODIPY functionalised epoxide activity based probe
ComponentsGlucosylceramidase
KeywordsHYDROLASE / beta-glucocerebrosidase / lysosomal glycoside hydrolase / GH30 / Cyclophellitol epoxide / activity based probe / Complex
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 / lymphocyte migration ...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 / lymphocyte migration / glucosylceramide catabolic process / regulation of lysosomal protein catabolic process / response to thyroid hormone / glucosylceramidase activity / sphingosine biosynthetic process / autophagosome organization / lysosomal protein catabolic process / microglial cell proliferation / glucosyltransferase activity / regulation of TOR signaling / Glycosphingolipid catabolism / microglia differentiation / lipid storage / ceramide biosynthetic process / positive regulation of type 2 mitophagy / : / brain morphogenesis / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / response to pH / pyramidal neuron differentiation / negative regulation of protein metabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / lysosome organization / neuromuscular process / response to dexamethasone / hematopoietic stem cell proliferation / antigen processing and presentation / response to testosterone / Association of TriC/CCT with target proteins during biosynthesis / motor behavior / negative regulation of interleukin-6 production / homeostasis of number of cells / regulation of macroautophagy / establishment of skin barrier / negative regulation of protein-containing complex assembly / cholesterol metabolic process / mitophagy / cell maturation / negative regulation of MAPK cascade / lysosomal lumen / cellular response to starvation / determination of adult lifespan / respiratory electron transport chain / trans-Golgi network / autophagy / negative regulation of inflammatory response / response to estrogen / cellular response to tumor necrosis factor / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / T cell differentiation in thymus / neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / GUANIDINE / Chem-K35 / Chem-Q65 / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRowland, R.J. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
CitationJournal: 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
DepositionMay 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z
Revision 1.2Dec 8, 2021Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glucosylceramidase
BBB: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,57146
Polymers111,2802
Non-polymers5,29144
Water16,286904
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-97 kcal/mol
Surface area36370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.172, 285.622, 91.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-764-

HOH

21AAA-1040-

HOH

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Components

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Protein , 1 types, 2 molecules AAABBB

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


Mass: 55640.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Recombinan beta-glucocerebrosidase (Cerezyme) missing the 40 amino acid signalling sequence
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC, GLUC / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P04062, glucosylceramidase, Transferases; Glycosyltransferases; Hexosyltransferases, EC: 3.2.1.104

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Sugars , 2 types, 4 molecules

#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: obtained synthetically
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: 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.: 2 / Source method: obtained synthetically / 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

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Non-polymers , 8 types, 944 molecules

#4: Chemical ChemComp-Q65 / (1~{S},2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[4-[4-[(12~{R})-2,2-bis(fluoranyl)-4,6,10,12-tetramethyl-1,3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-4,6,9-trien-8-yl]butyl]-1,2,3-triazol-1-yl]methyl]-7-oxabicyclo[4.1.0]heptane-2,3,4-triol


Mass: 532.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H37BF2N5O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K35 / ~{N}-[(1~{R},2~{R},3~{R},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]pentanamide


Mass: 277.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H23NO6
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#9: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CH5N3
#10: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.95 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→103.82 Å / Num. obs: 159511 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Net I/σ(I): 13.3
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2 / Num. unique obs: 7828 / CC1/2: 0.761 / Rpim(I) all: 0.445

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NT0

2nt0


Resolution: 1.7→103.816 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.166 / WRfactor Rwork: 0.149 / SU B: 2.314 / SU ML: 0.068 / Average fsc free: 0.872 / Average fsc work: 0.8789 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1805 7997 5.014 %
Rwork0.1626 151487 -
all0.163 --
obs-159484 99.91 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.297 Å2
Baniso -1Baniso -2Baniso -3
1-3.633 Å20 Å20 Å2
2---1.26 Å20 Å2
3----2.373 Å2
Refinement stepCycle: LAST / Resolution: 1.7→103.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7840 0 331 904 9075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138475
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177610
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.67311556
X-RAY DIFFRACTIONr_angle_other_deg1.2881.59417682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26951039
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg3.541206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95221.96403
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.803101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10115.071283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.311543
X-RAY DIFFRACTIONr_chiral_restr0.0950.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021804
X-RAY DIFFRACTIONr_nbd_refined0.1970.21569
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.27113
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23958
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2695
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.150.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.213
X-RAY DIFFRACTIONr_nbd_other0.1680.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.250
X-RAY DIFFRACTIONr_mcbond_it1.1862.224019
X-RAY DIFFRACTIONr_mcbond_other1.1852.2194017
X-RAY DIFFRACTIONr_mcangle_it1.8863.3235033
X-RAY DIFFRACTIONr_mcangle_other1.8863.3235034
X-RAY DIFFRACTIONr_scbond_it1.8332.6074456
X-RAY DIFFRACTIONr_scbond_other1.8332.6074457
X-RAY DIFFRACTIONr_scangle_it2.9433.7956520
X-RAY DIFFRACTIONr_scangle_other2.9433.7956518
X-RAY DIFFRACTIONr_lrange_it4.89227.6119544
X-RAY DIFFRACTIONr_lrange_other4.89227.6099545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3115880.31511086X-RAY DIFFRACTION99.7778
1.744-1.7920.2986080.2910784X-RAY DIFFRACTION99.9737
1.792-1.8440.2685710.25610521X-RAY DIFFRACTION99.982
1.844-1.9010.2515110.23510291X-RAY DIFFRACTION100
1.901-1.9630.2155760.2029904X-RAY DIFFRACTION100
1.963-2.0320.1915020.1859614X-RAY DIFFRACTION99.9802
2.032-2.1080.1764480.1669288X-RAY DIFFRACTION100
2.108-2.1950.1724660.1558965X-RAY DIFFRACTION100
2.195-2.2920.1684600.1458622X-RAY DIFFRACTION99.978
2.292-2.4040.1664380.1458196X-RAY DIFFRACTION100
2.404-2.5340.1574130.1367808X-RAY DIFFRACTION99.9878
2.534-2.6880.1994000.1477417X-RAY DIFFRACTION99.9872
2.688-2.8730.1693750.1396974X-RAY DIFFRACTION100
2.873-3.1030.1652880.1386543X-RAY DIFFRACTION99.9561
3.103-3.3990.1663290.146004X-RAY DIFFRACTION99.9842
3.399-3.80.1582860.1425464X-RAY DIFFRACTION99.9479
3.8-4.3870.1422520.134825X-RAY DIFFRACTION99.7642
4.387-5.3720.152240.1294090X-RAY DIFFRACTION99.6765
5.372-7.5920.1791730.1723215X-RAY DIFFRACTION99.53
7.592-103.8160.165890.1821876X-RAY DIFFRACTION99.393

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