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- PDB-2jey: Mus musculus acetylcholinesterase in complex with HLo-7 -

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Basic information

Entry
Database: PDB / ID: 2jey
TitleMus musculus acetylcholinesterase in complex with HLo-7
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ACETYLCHOLINESTERASE / ALTERNATIVE SPLICING / OXIME / MOUSE / HLO-7 / SYNAPSE / MEMBRANE / NEUROTRANSMITTER DEGRADATION / MUS MUSCULUS / GLYCOPROTEIN / SERINE ESTERASE
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / positive regulation of axonogenesis / osteoblast development / acetylcholine catabolic process / acetylcholinesterase / cholinesterase activity / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process ...acetylcholine metabolic process / serine hydrolase activity / positive regulation of axonogenesis / osteoblast development / acetylcholine catabolic process / acetylcholinesterase / cholinesterase activity / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / acetylcholine binding / acetylcholinesterase activity / retina development in camera-type eye / regulation of receptor recycling / basement membrane / side of membrane / collagen binding / laminin binding / synapse assembly / synaptic cleft / neuromuscular junction / receptor internalization / response to insulin / nuclear envelope / positive regulation of cold-induced thermogenesis / presynaptic membrane / cell adhesion / postsynaptic membrane / membrane raft / endoplasmic reticulum lumen / axon / hydrolase activity / neuronal cell body / dendrite / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / : / extracellular region / membrane / 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
Chem-HLO / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEkstrom, F. / Astot, C. / Pang, Y.P.
CitationJournal: Clin.Pharmacol.Ther. / Year: 2007
Title: Novel Nerve-Agent Antidote Design Based on Crystallographic and Mass Spectrometric Analyses of Tabun-Conjugated Acetylcholinesterase in Complex with Antidotes.
Authors: Ekstrom, F.J. / Astot, C. / Pang, Y.
History
DepositionJan 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: 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 1.4May 12, 2021Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.5Dec 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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4135
Polymers120,4682
Non-polymers9453
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-1 kcal/mol
Surface area34930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.670, 108.450, 220.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60233.984 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): HEK293 / Production host: HOMO SAPIENS (human)
References: UniProt: P21836, acetylcholinesterase, carboxylesterase
#2: Chemical ChemComp-HLO / 1-[({2,4-BIS[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]-4-CARBAMOYLPYRIDINIUM


Mass: 331.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N5O4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
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: 3.8 Å3/Da / Density % sol: 70 %
Crystal growpH: 7 / Details: 27-30 & PEG750MME, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.082
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.082 Å / Relative weight: 1
ReflectionResolution: 2.7→29.88 Å / Num. obs: 51435 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.7→29.88 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.869 / SU B: 10.06 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1011 2 %RANDOM
Rwork0.206 ---
obs0.207 50356 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 67 162 8565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.96311821
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06551064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62322.861395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.363151255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2541572
X-RAY DIFFRACTIONr_chiral_restr0.1140.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.26241
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3340.26147
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2634
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7241.55377
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28828588
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84233696
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0454.53233
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.373 77
Rwork0.295 3665

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