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

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Basic information

Entry
Database: PDB / ID: 6ytp
TitleStructure of recombinant human beta-glucocerebrosidase in complex with azide tagged cyclophellitol epoxide inhibitor
ComponentsGlucosylceramidase
KeywordsHYDROLASE / beta-glucocerebrosidase / lysosomal glycoside hydrolase / GH30 / Cyclophellitol epoxide / Inhibitor / 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 / lipid storage / microglia differentiation / 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
Chem-PN8 / 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
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 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)115,81042
Polymers111,2802
Non-polymers4,53040
Water11,908661
1
AAA: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,84321
Polymers55,6401
Non-polymers2,20320
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,96721
Polymers55,6401
Non-polymers2,32720
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.890, 285.769, 91.674
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-753-

HOH

21AAA-932-

HOH

31AAA-935-

HOH

41BBB-877-

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: Recombinant human beta-glucocerebrosidase 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: 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: 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 , 5 types, 697 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PN8 / (1~{S},2~{R},3~{R},4~{S},5~{S})-4-[[($l^{5}-azanylidyne-$l^{5}-azanyl)amino]methyl]cyclohexane-1,2,3,5-tetrol


Mass: 204.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14N3O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1 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: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→68.202 Å / Num. obs: 156446 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.036 / Net I/σ(I): 12.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.614 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7654 / CC1/2: 0.538 / Rpim(I) all: 0.741

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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→68.202 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.803 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2121 7842 5.013 %
Rwork0.1859 --
all0.187 --
obs-156420 99.861 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.556 Å2
Baniso -1Baniso -2Baniso -3
1-4.941 Å20 Å20 Å2
2---2.094 Å20 Å2
3----2.848 Å2
Refinement stepCycle: LAST / Resolution: 1.7→68.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7819 0 277 661 8757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138476
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177571
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.66111576
X-RAY DIFFRACTIONr_angle_other_deg1.2791.58417599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.29351056
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg30.789207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86822.159403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78715.071283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6131541
X-RAY DIFFRACTIONr_chiral_restr0.0710.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021810
X-RAY DIFFRACTIONr_nbd_refined0.2060.21703
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.27142
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23949
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23501
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2521
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.213
X-RAY DIFFRACTIONr_nbd_other0.1780.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.229
X-RAY DIFFRACTIONr_mcbond_it1.9763.1414061
X-RAY DIFFRACTIONr_mcbond_other1.9753.1414061
X-RAY DIFFRACTIONr_mcangle_it2.9894.7085100
X-RAY DIFFRACTIONr_mcangle_other2.9894.7085101
X-RAY DIFFRACTIONr_scbond_it2.5693.5694415
X-RAY DIFFRACTIONr_scbond_other2.573.574414
X-RAY DIFFRACTIONr_scangle_it4.0095.2216476
X-RAY DIFFRACTIONr_scangle_other4.0095.2216476
X-RAY DIFFRACTIONr_lrange_it6.00937.8399459
X-RAY DIFFRACTIONr_lrange_other6.0137.8369458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.4146010.41410824X-RAY DIFFRACTION99.8165
1.744-1.7920.3765640.37610620X-RAY DIFFRACTION100
1.792-1.8440.3725620.34910357X-RAY DIFFRACTION99.9817
1.844-1.9010.3175090.31610076X-RAY DIFFRACTION99.9717
1.901-1.9630.285590.289687X-RAY DIFFRACTION99.9805
1.963-2.0320.2694850.2559455X-RAY DIFFRACTION99.9497
2.032-2.1080.2294410.2199141X-RAY DIFFRACTION100
2.108-2.1950.2284600.28793X-RAY DIFFRACTION99.9568
2.195-2.2920.2344540.188451X-RAY DIFFRACTION99.9888
2.292-2.4040.2044300.1738032X-RAY DIFFRACTION100
2.404-2.5340.2144170.1677666X-RAY DIFFRACTION99.9753
2.534-2.6880.2153800.1677279X-RAY DIFFRACTION100
2.688-2.8730.1983640.1596869X-RAY DIFFRACTION100
2.873-3.1030.1912900.1576406X-RAY DIFFRACTION99.9851
3.103-3.3990.1833230.1565901X-RAY DIFFRACTION99.9679
3.399-3.80.1742800.1525333X-RAY DIFFRACTION99.7689
3.8-4.3870.1572500.1324719X-RAY DIFFRACTION99.659
4.387-5.3720.1452210.1244011X-RAY DIFFRACTION99.4595
5.372-7.5920.2071630.1613138X-RAY DIFFRACTION98.8619
7.592-68.2020.185890.1771820X-RAY DIFFRACTION98.3007

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