[English] 日本語
Yorodumi
- PDB-6yv3: Structure of recombinant human beta-glucocerebrosidase in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yv3
TitleStructure of recombinant human beta-glucocerebrosidase in complex with galacto-configured cyclophellitol aziridine inhibitor
ComponentsGlucosylceramidase
KeywordsHYDROLASE / beta-glucocerebrosidase / lysosomal glycoside hydrolase / GH30 / Cyclophellitol aziridine / 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 / 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-UUU / 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
DepositionApr 27, 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 2.0Dec 8, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / 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 2.1Jan 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 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Glucosylceramidase
BBB: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,72940
Polymers111,2802
Non-polymers4,44938
Water15,403855
1
AAA: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,55915
Polymers55,6401
Non-polymers1,91914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,17025
Polymers55,6401
Non-polymers2,53024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.556, 285.273, 91.830
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-1002-

HOH

21AAA-1012-

HOH

31BBB-779-

HOH

-
Components

-
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 lacking its 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

-
Sugars , 2 types, 6 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.: 4
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

-
Non-polymers , 6 types, 887 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-UUU / (1S,2S,3S,4S,5R,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 193.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 855 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→72.197 Å / Num. obs: 134042 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.052 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.364 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6543 / CC1/2: 0.59 / Rpim(I) all: 0.848 / % possible all: 100

-
Processing

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

2nt0


Resolution: 1.8→72.197 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.326 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2032 6677 4.982 %
Rwork0.1755 --
all0.177 --
obs-134017 99.884 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.029 Å2
Baniso -1Baniso -2Baniso -3
1-3.874 Å20 Å20 Å2
2---1.618 Å20 Å2
3----2.257 Å2
Refinement stepCycle: LAST / Resolution: 1.8→72.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7791 0 269 855 8915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138410
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177533
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.66811489
X-RAY DIFFRACTIONr_angle_other_deg1.2951.5917505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17251054
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg1.632208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46522.01398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315.0941280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4051542
X-RAY DIFFRACTIONr_chiral_restr0.0730.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021791
X-RAY DIFFRACTIONr_nbd_refined0.2040.21659
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.26939
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23917
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2614
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.215
X-RAY DIFFRACTIONr_nbd_other0.2010.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.236
X-RAY DIFFRACTIONr_mcbond_it1.8712.724029
X-RAY DIFFRACTIONr_mcbond_other1.872.724028
X-RAY DIFFRACTIONr_mcangle_it2.9144.0675052
X-RAY DIFFRACTIONr_mcangle_other2.9144.0675053
X-RAY DIFFRACTIONr_scbond_it2.6383.184381
X-RAY DIFFRACTIONr_scbond_other2.6383.184382
X-RAY DIFFRACTIONr_scangle_it4.2194.6456437
X-RAY DIFFRACTIONr_scangle_other4.2194.6456438
X-RAY DIFFRACTIONr_lrange_it6.29933.4049467
X-RAY DIFFRACTIONr_lrange_other6.29933.4049468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3594960.3479276X-RAY DIFFRACTION99.8365
1.847-1.8970.3064510.3119166X-RAY DIFFRACTION99.9896
1.897-1.9520.2915190.2868789X-RAY DIFFRACTION99.9893
1.952-2.0120.2464740.2418596X-RAY DIFFRACTION99.978
2.012-2.0780.2283920.2158396X-RAY DIFFRACTION99.9886
2.078-2.1510.2323980.1978095X-RAY DIFFRACTION99.9529
2.151-2.2320.2224270.1867809X-RAY DIFFRACTION99.9879
2.232-2.3240.214050.1777485X-RAY DIFFRACTION99.962
2.324-2.4270.1963770.1617218X-RAY DIFFRACTION99.9605
2.427-2.5450.1913730.1556917X-RAY DIFFRACTION100
2.545-2.6830.2143450.166563X-RAY DIFFRACTION99.9566
2.683-2.8460.1793380.1536214X-RAY DIFFRACTION99.726
2.846-3.0420.1972590.1625906X-RAY DIFFRACTION99.919
3.042-3.2860.2032910.1655470X-RAY DIFFRACTION99.948
3.286-3.5990.1952670.1595030X-RAY DIFFRACTION99.9057
3.599-4.0240.1692330.144602X-RAY DIFFRACTION99.8142
4.024-4.6450.1372240.1224057X-RAY DIFFRACTION99.6276
4.645-5.6880.1871980.1423442X-RAY DIFFRACTION99.8354
5.688-8.0370.1771340.1752724X-RAY DIFFRACTION99.7557
8.037-72.1970.216760.1871585X-RAY DIFFRACTION99.4611

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more