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- PDB-4aqd: Crystal structure of fully glycosylated human butyrylcholinesterase -

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Basic information

Entry
Database: PDB / ID: 4aqd
TitleCrystal structure of fully glycosylated human butyrylcholinesterase
ComponentsBUTYRYLCHOLINESTERASE
KeywordsHYDROLASE / ACETYLCHOLINESTERASE / EXPRESSION / HUPRINE / SERINE HYDROLASE / CATALYTIC TRIAD / INSECT CELLS / GLYCOSYLATIONS
Function / homology
Function and homology information


cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / acetylcholine catabolic process ...cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / hydrolase activity, acting on ester bonds / acetylcholinesterase activity / Aspirin ADME / Synthesis of PC / nuclear envelope lumen / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / xenobiotic metabolic process / response to glucocorticoid / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-ALANINE / GLYCINE / DI(HYDROXYETHYL)ETHER / Cholinesterase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBrazzolotto, X. / Wandhammer, M. / Ronco, C. / Trovaslet, M. / Jean, L. / Lockridge, O. / Renard, P.Y. / Nachon, F.
CitationJournal: FEBS J. / Year: 2012
Title: Human butyrylcholinesterase produced in insect cells: huprine-based affinity purification and crystal structure.
Authors: Brazzolotto, X. / Wandhammer, M. / Ronco, C. / Trovaslet, M. / Jean, L. / Lockridge, O. / Renard, P.Y. / Nachon, F.
History
DepositionApr 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Nov 20, 2013Group: Derived calculations
Revision 1.3Nov 14, 2018Group: Advisory / Data collection / Database references
Category: citation / database_PDB_caveat / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
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.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BUTYRYLCHOLINESTERASE
B: BUTYRYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,34661
Polymers119,8032
Non-polymers8,54259
Water5,008278
1
A: BUTYRYLCHOLINESTERASE
hetero molecules

B: BUTYRYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,34661
Polymers119,8032
Non-polymers8,54259
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
2
A: BUTYRYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,48729
Polymers59,9021
Non-polymers4,58628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: BUTYRYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,85832
Polymers59,9021
Non-polymers3,95731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.750, 79.260, 227.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BUTYRYLCHOLINESTERASE


Mass: 59901.672 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMT-BIP / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P06276, cholinesterase

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Sugars , 4 types, 15 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: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 6
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 , 8 types, 322 molecules

#5: Chemical ChemComp-BAL / BETA-ALANINE


Type: peptide-like / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#10: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#12: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7.4
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 3350, 0.2 M NH4OAC PH 7.4, AT 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2011
RadiationMonochromator: SILICON (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.5→39 Å / Num. obs: 46071 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 46.58 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P0I

1p0i


Resolution: 2.5→39.041 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 22.76 / Stereochemistry target values: ML
Details: A BETA-ALANINE WAS MODELED AT BOND DISTANCE TO THE CATALYTIC SERINE. A PEAK OF ELECTRON DENSITY CLOSE TO A PEAK OF ELECTRON DENSITY CLOSE TO TRP82 WAS MODELED AS DUMMY ATOMS (RESIDUES UNX).
RfactorNum. reflection% reflection
Rfree0.232 1381 3 %
Rwork0.1632 --
obs0.1652 46071 99.39 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.675 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5507 Å20 Å20 Å2
2---5.2688 Å20 Å2
3---0.7181 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8390 0 562 278 9230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089212
X-RAY DIFFRACTIONf_angle_d1.23112488
X-RAY DIFFRACTIONf_dihedral_angle_d22.7263471
X-RAY DIFFRACTIONf_chiral_restr0.0771386
X-RAY DIFFRACTIONf_plane_restr0.0051550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.58950.31351330.24534308X-RAY DIFFRACTION98
2.5895-2.69320.32171370.21424426X-RAY DIFFRACTION99
2.6932-2.81570.24461360.18624399X-RAY DIFFRACTION100
2.8157-2.96410.24771360.1724412X-RAY DIFFRACTION100
2.9641-3.14980.25761380.16364461X-RAY DIFFRACTION100
3.1498-3.39280.2791380.16914439X-RAY DIFFRACTION100
3.3928-3.7340.2371380.16374464X-RAY DIFFRACTION100
3.734-4.27380.19911400.13944533X-RAY DIFFRACTION100
4.2738-5.38230.19781400.13664532X-RAY DIFFRACTION100
5.3823-39.04530.21531450.17084716X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.842-0.1064-0.35742.05590.04011.758-0.0176-0.3549-0.25660.2116-0.00290.09950.28220.097-0.01730.255-0.0305-0.00730.22970.07930.164-10.8838-10.3045-8.4504
22.3869-0.5403-0.78711.87590.50152.4847-0.0004-0.06520.0247-0.22490.0287-0.204-0.11540.3819-0.00390.2518-0.0554-0.0240.14380.03320.08414.27550.705-25.0057
32.20060.7362-0.14163.2124-0.66672.45150.1855-0.01790.13130.27220.01930.5592-0.0716-0.4262-0.08810.21160.013-0.02290.21440.00150.2053-31.912725.0871-37.2007
41.48760.5247-0.44381.7886-0.33962.65210.08270.2510.4237-0.49970.06290.0607-0.72990.065-0.05010.5127-0.0139-0.05710.12280.10.2338-16.256737.8569-51.8162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:315)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 316:529)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 4:315)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 316:529)

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