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- PDB-4bc1: Structure of mouse acetylcholinesterase inhibited by CBDP (30-min... -

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Basic information

Entry
Database: PDB / ID: 4bc1
TitleStructure of mouse acetylcholinesterase inhibited by CBDP (30-min soak): cresyl-saligenin-phosphoserine adduct
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / BUTYRYLCHOLINESTERASE / NERVE TRANSMISSION / INHIBITOR / ALPHA-BETA HYDROLASE
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis ...acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / laminin binding / side of membrane / synapse assembly / collagen binding / neuromuscular junction / response to insulin / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / hydrolase activity / cell adhesion / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / 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
O-CRESYL-SALIGENIN PHOSPHATE / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCarletti, E. / Colletier, J.-P. / Schopfer, L.M. / Santoni, G. / Masson, P. / Lockridge, O. / Nachon, F. / Weik, M.
CitationJournal: Chem.Res.Toxicol. / Year: 2013
Title: Inhibition Pathways of the Potent Organophosphate Cbdp with Cholinesterases Revealed by X-Ray Crystallographic Snapshots and Mass Spectrometry
Authors: Carletti, E. / Colletier, J.-P. / Schopfer, L.M. / Santoni, G. / Masson, P. / Lockridge, O. / Nachon, F. / Weik, M.
History
DepositionSep 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
C: ACETYLCHOLINESTERASE
D: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,61441
Polymers239,0584
Non-polymers4,55637
Water15,043835
1
A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,96312
Polymers59,7641
Non-polymers1,19811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8258
Polymers59,7641
Non-polymers1,0607
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,71010
Polymers59,7641
Non-polymers9459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,11711
Polymers59,7641
Non-polymers1,35210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.540, 173.250, 224.940
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 / Sugars , 2 types, 11 molecules ABCD

#1: Protein
ACETYLCHOLINESTERASE / / ACHE


Mass: 59764.488 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Details: CRESYL-SALIGENIN-PHOSPHATE ADDUCT ON S203 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGS / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P21836, acetylcholinesterase
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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, 865 molecules

#2: Chemical
ChemComp-TQV / O-CRESYL-SALIGENIN PHOSPHATE


Mass: 294.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15O5P
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H2O

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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: 5.5 Å3/Da / Density % sol: 78 % / Description: NONE
Crystal growpH: 7.4
Details: 0.1 M TRIS HCL BUFFER PH 7.4, 1.6 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.95→48.3 Å / Num. obs: 111473 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 63.89 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.95→3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A16

4a16


Resolution: 2.95→48.285 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 3344 3 %
Rwork0.1863 --
obs0.1879 111450 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.8 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16791 0 260 835 17886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917683
X-RAY DIFFRACTIONf_angle_d1.36824190
X-RAY DIFFRACTIONf_dihedral_angle_d16.4986363
X-RAY DIFFRACTIONf_chiral_restr0.0852580
X-RAY DIFFRACTIONf_plane_restr0.0073171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.99210.37061370.32794428X-RAY DIFFRACTION99
2.9921-3.03680.3941370.32454434X-RAY DIFFRACTION99
3.0368-3.08420.37561380.30614470X-RAY DIFFRACTION99
3.0842-3.13480.36271360.29424402X-RAY DIFFRACTION99
3.1348-3.18880.37211380.28964456X-RAY DIFFRACTION99
3.1888-3.24680.32621380.27374456X-RAY DIFFRACTION99
3.2468-3.30920.32641380.2624477X-RAY DIFFRACTION99
3.3092-3.37680.31380.24934441X-RAY DIFFRACTION100
3.3768-3.45020.28921380.23314481X-RAY DIFFRACTION100
3.4502-3.53040.27971380.21994464X-RAY DIFFRACTION100
3.5304-3.61870.24931390.20144486X-RAY DIFFRACTION100
3.6187-3.71650.27331390.19434481X-RAY DIFFRACTION100
3.7165-3.82580.24661380.18264489X-RAY DIFFRACTION100
3.8258-3.94920.22521400.16884523X-RAY DIFFRACTION100
3.9492-4.09030.22641390.15854495X-RAY DIFFRACTION100
4.0903-4.2540.19751400.15214515X-RAY DIFFRACTION100
4.254-4.44750.18751390.13884504X-RAY DIFFRACTION100
4.4475-4.68180.18511410.13244544X-RAY DIFFRACTION100
4.6818-4.97480.20691400.1314520X-RAY DIFFRACTION100
4.9748-5.35850.19461400.14324548X-RAY DIFFRACTION100
5.3585-5.89690.18881410.14314547X-RAY DIFFRACTION100
5.8969-6.74820.19111420.15874581X-RAY DIFFRACTION100
6.7482-8.49440.19911420.15634599X-RAY DIFFRACTION99
8.4944-48.29130.20081480.18724765X-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)
10.91620.4194-0.1652.1128-0.24061.0856-0.04420.103-0.00330.10790.05760.0157-0.1221-0.08160.01730.1548-0.03640.02980.1658-0.01910.14235.7557-28.87886.0218
21.0905-0.32940.31881.2305-0.45041.1011-0.1406-0.3003-0.0840.54650.3940.3852-0.6049-0.91640.1820.68640.49230.21240.42580.07730.3489-8.522626.953466.2992
30.8768-0.01730.22841.2883-0.08871.7093-0.0958-0.0109-0.05890.0867-0.0237-0.1211-0.07230.2718-0.09730.14240.02440.0850.12550.05860.153224.142912.117924.9778
41.1412-0.12530.32341.1683-0.27482.1933-0.0340.21160.1893-0.0537-0.1228-0.2087-0.07860.3692-0.13440.1774-0.0543-0.06390.30810.11190.277947.66185.498580.7386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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