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- PDB-6z3i: Structure of recombinant beta-glucocerebrosidase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6z3i
TitleStructure of recombinant beta-glucocerebrosidase in complex with bifunctional cyclophellitol aziridine activity based probe
ComponentsLysosomal acid glucosylceramidase
KeywordsHYDROLASE / lysosomal hydrolase / activity based probe
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 / sphingosine biosynthetic process / autophagosome organization / glucosylceramidase activity / microglial cell proliferation / lysosomal protein catabolic process / 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 / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-Q68 / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 20, 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
BBB: Lysosomal acid glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,61125
Polymers55,6591
Non-polymers2,95224
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint2 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.139, 76.670, 67.988
Angle α, β, γ (deg.)90.000, 102.053, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules BBB

#1: Protein Lysosomal acid glucosylceramidase / Lysosomal acid GCase / Acid beta-glucosidase / Alglucerase / Beta-glucocerebrosidase / Beta-GC / ...Lysosomal acid GCase / Acid beta-glucosidase / Alglucerase / Beta-glucocerebrosidase / Beta-GC / Cholesterol glucosyltransferase / SGTase / Cholesteryl-beta-glucosidase / D-glucosyl-N-acylsphingosine glucohydrolase / Imiglucerase


Mass: 55659.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Recombinant human beta-glucocerebrosidase lacking its 40 amino acid signalling sequence produced in insect cells
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC, GLUC / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P04062, glucosylceramidase, Transferases; Glycosyltransferases; Hexosyltransferases, EC: 3.2.1.104

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Sugars , 2 types, 3 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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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: 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

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Non-polymers , 4 types, 359 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Chemical ChemComp-Q68 / ~{N}-[[1-[[(1~{S},2~{R},3~{R},4~{S},6~{S})-6-(hexylamino)-2,3,4-tris(oxidanyl)cyclohexyl]methyl]-1,2,3-triazol-4-yl]methyl]ethanamide


Mass: 383.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C18H33N5O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na2SO4, 0.25 M HEPES pH 7, PEG3350 14%, 1:1000 seed

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979507 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979507 Å / Relative weight: 1
ReflectionResolution: 1.8→76.67 Å / Num. obs: 49541 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.084 / Net I/σ(I): 6.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.351 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2966 / CC1/2: 0.506 / Rpim(I) all: 1.301 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TJK

6tjk


Resolution: 1.8→66.578 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.163 / SU B: 3.598 / SU ML: 0.098 / Average fsc free: 0.8785 / Average fsc work: 0.8756 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1894 2509 5.067 %
Rwork0.1782 47010 -
all0.179 --
obs-49519 99.962 %
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: 25.448 Å2
Baniso -1Baniso -2Baniso -3
1-1.832 Å20 Å21.153 Å2
2--0.507 Å20 Å2
3----2.595 Å2
Refinement stepCycle: LAST / Resolution: 1.8→66.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3922 0 189 338 4449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134279
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173871
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.6845813
X-RAY DIFFRACTIONr_angle_other_deg1.251.68979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4875512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29121.893206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02515.016636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9411523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
X-RAY DIFFRACTIONr_nbd_refined0.2030.2833
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23745
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21978
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2321
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.224
X-RAY DIFFRACTIONr_nbd_other0.2340.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.212
X-RAY DIFFRACTIONr_mcbond_it1.0722.532016
X-RAY DIFFRACTIONr_mcbond_other1.0692.5292014
X-RAY DIFFRACTIONr_mcangle_it1.6343.7912527
X-RAY DIFFRACTIONr_mcangle_other1.6343.7922528
X-RAY DIFFRACTIONr_scbond_it1.5232.8422263
X-RAY DIFFRACTIONr_scbond_other1.5232.8432264
X-RAY DIFFRACTIONr_scangle_it2.3554.1683286
X-RAY DIFFRACTIONr_scangle_other2.3554.1693287
X-RAY DIFFRACTIONr_lrange_it3.83230.7614765
X-RAY DIFFRACTIONr_lrange_other3.66630.4344693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3231800.3413474X-RAY DIFFRACTION99.9726
1.847-1.8970.2961730.3083417X-RAY DIFFRACTION100
1.897-1.9520.3081680.2843240X-RAY DIFFRACTION100
1.952-2.0120.2621560.2593211X-RAY DIFFRACTION100
2.012-2.0780.2451670.2263081X-RAY DIFFRACTION100
2.078-2.1510.2241590.2152989X-RAY DIFFRACTION100
2.151-2.2320.2161480.1962884X-RAY DIFFRACTION100
2.232-2.3230.1741530.1772814X-RAY DIFFRACTION100
2.323-2.4270.2021510.1742655X-RAY DIFFRACTION100
2.427-2.5450.1691500.1632525X-RAY DIFFRACTION100
2.545-2.6820.1891260.1562411X-RAY DIFFRACTION100
2.682-2.8450.1551300.1552309X-RAY DIFFRACTION100
2.845-3.0410.1981160.1462139X-RAY DIFFRACTION100
3.041-3.2840.1641050.1482027X-RAY DIFFRACTION100
3.284-3.5970.181050.1541844X-RAY DIFFRACTION100
3.597-4.020.167760.1441707X-RAY DIFFRACTION100
4.02-4.640.146820.1291475X-RAY DIFFRACTION100
4.64-5.6780.119710.1341267X-RAY DIFFRACTION100
5.678-8.0080.163590.174974X-RAY DIFFRACTION99.9033
8.008-66.5780.156340.176567X-RAY DIFFRACTION99.8339

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