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- PDB-2wls: Crystal structure of Mus musculus Acetylcholinesterase in complex... -

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Basic information

Entry
Database: PDB / ID: 2wls
TitleCrystal structure of Mus musculus Acetylcholinesterase in complex with AMTS13
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / SERINE ESTERASE / ALTERNATIVE SPLICING / AMTS13 / SYNAPSE / MEMBRANE / CELL MEMBRANE / CHOLINESTERASE / ACETYLCHOLINESTERASE / NEUROTRANSMITTER DEGRADATION / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / CELL JUNCTION
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / 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
DI(HYDROXYETHYL)ETHER / Chem-X13 / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPang, Y.P. / Ekstrom, F. / Polsinelli, G.A. / Gao, Y. / Rana, S. / Hua, D.H. / Andersson, B. / Andersson, P.O. / Peng, L. / Singh, S.K. ...Pang, Y.P. / Ekstrom, F. / Polsinelli, G.A. / Gao, Y. / Rana, S. / Hua, D.H. / Andersson, B. / Andersson, P.O. / Peng, L. / Singh, S.K. / Mishra, R.K. / Zhu, K.Y. / Fallon, A.M. / Ragsdale, D.W. / Brimijoin, S.
CitationJournal: Plos One / Year: 2009
Title: Selective and Irreversible Inhibitors of Mosquito Acetylcholinesterases for Controlling Malaria and Other Mosquito-Borne Diseases.
Authors: Pang, Y.P. / Ekstrom, F. / Polsinelli, G.A. / Gao, Y. / Rana, S. / Hua, D.H. / Andersson, B. / Andersson, P.O. / Peng, L. / Singh, S.K. / Mishra, R.K. / Zhu, K.Y. / Fallon, A.M. / Ragsdale, D.W. / Brimijoin, S.
History
DepositionJun 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.pdbx_synonyms
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0658
Polymers119,5292
Non-polymers1,5366
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-0 kcal/mol
Surface area37270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.480, 110.305, 227.604
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, 4 molecules AB

#1: Protein ACETYLCHOLINESTERASE


Mass: 59764.488 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase
#2: 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, 353 molecules

#3: Chemical ChemComp-X13 / N,N,N-trimethyl-13-[(methylsulfonyl)sulfanyl]tridecan-1-aminium


Mass: 352.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H38NO2S2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsN,N,N-TRIMETHYL-13-(METHYLSULFONYLTHIO)TRIDECAN-1-AMINIUM BROMIDE (A13): COMPUND REPORTED IN PANG Y- ...N,N,N-TRIMETHYL-13-(METHYLSULFONYLTHIO)TRIDECAN-1-AMINIUM BROMIDE (A13): COMPUND REPORTED IN PANG Y-P, SINGH SK, GAO Y, LASSITER TL, MISHRA RK, ET AL.2009 SELECTIVE AND IRREVERSIBLE INHIBITORS OF APHID ACETYLCHOLINESTERASES STEPS TOWARD HUMAN-SAFE INSECTICIDES. PLOS ONE 4 E4349.

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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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.948
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.6→29 Å / Num. obs: 61580 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Biso Wilson estimate: 60.66 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.6→29.037 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 22.53 / Stereochemistry target values: ML / Details: THE SO2CH3 GROUP OF AMTS13 IS UNDEFINED
RfactorNum. reflection% reflection
Rfree0.2261 1220 2 %
Rwork0.1851 --
obs0.1859 61249 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.005 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8455 Å20 Å2-0 Å2
2--2.0636 Å2-0 Å2
3----2.9091 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8321 0 90 349 8760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088703
X-RAY DIFFRACTIONf_angle_d1.13311873
X-RAY DIFFRACTIONf_dihedral_angle_d18.4613116
X-RAY DIFFRACTIONf_chiral_restr0.0751281
X-RAY DIFFRACTIONf_plane_restr0.0061557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70410.30731460.25096617X-RAY DIFFRACTION100
2.7041-2.8270.31941350.24086573X-RAY DIFFRACTION100
2.827-2.97590.30951300.22976615X-RAY DIFFRACTION100
2.9759-3.16220.29561550.22566608X-RAY DIFFRACTION100
3.1622-3.4060.20751160.19556671X-RAY DIFFRACTION100
3.406-3.74810.21851430.17896641X-RAY DIFFRACTION100
3.7481-4.2890.20351250.15916616X-RAY DIFFRACTION99
4.289-5.3980.17991330.14546736X-RAY DIFFRACTION99
5.398-29.03860.18761370.17236952X-RAY DIFFRACTION99

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