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- PDB-6tjq: Crystal Structure of Recombinant GBA in Complex with 2-Deoxy-2-fl... -

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Basic information

Entry
Database: PDB / ID: 6tjq
TitleCrystal Structure of Recombinant GBA in Complex with 2-Deoxy-2-fluoro-beta-D-glucopyranoside
ComponentsGlucosylceramidase
KeywordsHYDROLASE / beta-glucocerebrosidase / lysosomal glycoside hydrolase / GH30
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
Chem-NF8 / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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 / 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 / pdbx_validate_close_contact / pdbx_validate_symm_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 / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 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: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,45626
Polymers55,6591
Non-polymers2,79725
Water8,521473
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint8 kcal/mol
Surface area18670 Å2
Unit cell
Length a, b, c (Å)53.112, 76.351, 68.160
Angle α, β, γ (deg.)90.000, 101.987, 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 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: 55659.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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, 495 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.: 17
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Chemical ChemComp-NF8 / (2~{R},3~{S},4~{S},5~{S})-5-fluoranyl-2-(hydroxymethyl)oxane-3,4-diol


Mass: 166.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11FO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.41→51.95 Å / Num. obs: 102363 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.056 / Net I/σ(I): 7.2
Reflection shellResolution: 1.41→7.72 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5031 / CC1/2: 0.357 / Rpim(I) all: 2.388

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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: 1.41→51.95 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.084 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2053 4992 4.879 %
Rwork0.1776 --
all0.179 --
obs-102326 99.9 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.462 Å20 Å20.748 Å2
2--1.266 Å20 Å2
3----1.876 Å2
Refinement stepCycle: LAST / Resolution: 1.41→51.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 177 473 4573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134371
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173947
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6755948
X-RAY DIFFRACTIONr_angle_other_deg1.3581.599176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.8965.519559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68421.787207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01915.016640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.581523
X-RAY DIFFRACTIONr_chiral_restr0.0750.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025469
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02937
X-RAY DIFFRACTIONr_nbd_refined0.2080.2847
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23778
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22045
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.21814
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2390
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1640.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.219
X-RAY DIFFRACTIONr_nbd_other0.2340.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.230
X-RAY DIFFRACTIONr_mcbond_it1.1361.9882072
X-RAY DIFFRACTIONr_mcbond_other1.1361.9872071
X-RAY DIFFRACTIONr_mcangle_it1.6372.982618
X-RAY DIFFRACTIONr_mcangle_other1.6372.9812619
X-RAY DIFFRACTIONr_scbond_it1.7422.3062299
X-RAY DIFFRACTIONr_scbond_other1.7412.3072300
X-RAY DIFFRACTIONr_scangle_it2.5963.3623330
X-RAY DIFFRACTIONr_scangle_other2.5953.3643331
X-RAY DIFFRACTIONr_lrange_it4.6625.0674950
X-RAY DIFFRACTIONr_lrange_other4.39924.3644822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.4470.423730.4037131X-RAY DIFFRACTION99.5357
1.447-1.4860.3554070.3746960X-RAY DIFFRACTION99.7833
1.486-1.5290.353470.3466762X-RAY DIFFRACTION99.8315
1.529-1.5760.3113440.3166630X-RAY DIFFRACTION99.914
1.576-1.6280.3063360.2916363X-RAY DIFFRACTION99.9851
1.628-1.6850.2882940.2616210X-RAY DIFFRACTION99.9846
1.685-1.7490.2492890.2346030X-RAY DIFFRACTION100
1.749-1.820.2422970.215764X-RAY DIFFRACTION100
1.82-1.9010.22790.1855550X-RAY DIFFRACTION100
1.901-1.9940.1992610.1635261X-RAY DIFFRACTION100
1.994-2.1010.2182350.1625074X-RAY DIFFRACTION100
2.101-2.2290.1822400.1474759X-RAY DIFFRACTION100
2.229-2.3830.1742690.1344442X-RAY DIFFRACTION99.9788
2.383-2.5730.1692050.1324174X-RAY DIFFRACTION100
2.573-2.8190.1811850.133859X-RAY DIFFRACTION100
2.819-3.1510.1711790.1373474X-RAY DIFFRACTION100
3.151-3.6370.1611380.1383111X-RAY DIFFRACTION100
3.637-4.4520.1541380.1292617X-RAY DIFFRACTION100
4.452-6.2850.1691140.1392009X-RAY DIFFRACTION100
6.285-51.950.185620.1761154X-RAY DIFFRACTION99.9178

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