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- PDB-6tjj: Structure of Cerezyme at pH 4.6 -

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Basic information

Entry
Database: PDB / ID: 6tjj
TitleStructure of Cerezyme at pH 4.6
ComponentsGlucosylceramidase
KeywordsHYDROLASE / beta-glucocerebrosidase / lysosomal glycoside hydrolase / GH30
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 / cellular response to starvation / respiratory electron transport chain / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / : / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsRowland, R.J. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: A baculoviral system for the production of human beta-glucocerebrosidase enables atomic resolution analysis.
Authors: Rowland, R.J. / Wu, L. / Liu, F. / Davies, G.J.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / exptl_crystal / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn
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.occupancy / _atom_site.type_symbol / _chem_comp.name / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)115,30742
Polymers111,2802
Non-polymers4,02740
Water12,881715
1
AAA: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,75621
Polymers55,6401
Non-polymers2,11620
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,55221
Polymers55,6401
Non-polymers1,91220
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.070, 285.865, 91.936
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
11BBB-958-

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 / Mutation: H495R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC, GLUC / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P04062, glucosylceramidase, Transferases; Glycosyltransferases; Hexosyltransferases, steryl-beta-glucosidase

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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
#5: 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 / N-Acetylglucosamine


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 , 5 types, 751 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.1 M (NH4)2SO4, 0.19 M guanidine HCl, 0.04 M KCl, 0.1 M Na 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 X 16M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.59→142.93 Å / Num. all: 1531796 / Num. obs: 193710 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.055 / Net I/σ(I): 7.2
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 7.9 % / Rmerge(I) obs: 6.202 / Mean I/σ(I) obs: 0.5 / Num. unique all: 74996 / Num. unique obs: 9517 / CC1/2: 0.676 / Rpim(I) all: 2.348

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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: 1.59→77.442 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.203 / SU B: 4.812 / SU ML: 0.134 / Average fsc free: 0.642 / Average fsc work: 0.6546 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2448 9698 5.008 %
Rwork0.2146 183970 -
all0.216 --
obs-193668 99.956 %
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: 32.082 Å2
Baniso -1Baniso -2Baniso -3
1-4.921 Å20 Å2-0 Å2
2---1.64 Å20 Å2
3----3.281 Å2
Refinement stepCycle: LAST / Resolution: 1.59→77.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7833 0 240 715 8788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138488
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177557
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.65411606
X-RAY DIFFRACTIONr_angle_other_deg1.361.5817540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57851060
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg35.453208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17821.932414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73715.0691296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1461545
X-RAY DIFFRACTIONr_chiral_restr0.0820.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029524
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021833
X-RAY DIFFRACTIONr_nbd_refined0.2080.21714
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.27013
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23932
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.23488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2504
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.218
X-RAY DIFFRACTIONr_nbd_other0.170.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.231
X-RAY DIFFRACTIONr_mcbond_it2.5143.1264086
X-RAY DIFFRACTIONr_mcbond_other2.4643.1194075
X-RAY DIFFRACTIONr_mcangle_it3.4354.6665116
X-RAY DIFFRACTIONr_mcangle_other3.4394.6675117
X-RAY DIFFRACTIONr_scbond_it3.5473.6684402
X-RAY DIFFRACTIONr_scbond_other3.5463.6694403
X-RAY DIFFRACTIONr_scangle_it5.4385.3666490
X-RAY DIFFRACTIONr_scangle_other5.4385.3666491
X-RAY DIFFRACTIONr_lrange_it7.36138.0049457
X-RAY DIFFRACTIONr_lrange_other7.34537.6769334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.6310.4447650.46113446X-RAY DIFFRACTION99.9086
1.631-1.6760.4346890.43913150X-RAY DIFFRACTION99.9928
1.676-1.7250.3946470.4112823X-RAY DIFFRACTION99.9852
1.725-1.7780.3896480.38712452X-RAY DIFFRACTION99.9924
1.778-1.8360.3666250.3612110X-RAY DIFFRACTION99.9686
1.836-1.90.3325920.33111701X-RAY DIFFRACTION100
1.9-1.9720.3076070.31211229X-RAY DIFFRACTION99.9747
1.972-2.0530.2835440.25810893X-RAY DIFFRACTION100
2.053-2.1440.2625270.22910435X-RAY DIFFRACTION99.9909
2.144-2.2480.2945120.24210010X-RAY DIFFRACTION99.9905
2.248-2.370.2574940.2089500X-RAY DIFFRACTION99.99
2.37-2.5140.2394960.1918995X-RAY DIFFRACTION100
2.514-2.6870.2474500.1968458X-RAY DIFFRACTION100
2.687-2.9020.2574280.1957872X-RAY DIFFRACTION99.9759
2.902-3.1790.2213790.1847294X-RAY DIFFRACTION99.987
3.179-3.5540.2193660.1766614X-RAY DIFFRACTION99.9857
3.554-4.1040.1913100.1485858X-RAY DIFFRACTION99.9676
4.104-5.0250.1462900.1244954X-RAY DIFFRACTION100
5.025-7.1020.1941990.1553929X-RAY DIFFRACTION100
7.102-77.4420.1941300.1762248X-RAY DIFFRACTION99.916

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