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- PDB-8dt4: X-ray structure of human acetylcholinesterase ternary complex wit... -

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Basic information

Entry
Database: PDB / ID: 8dt4
TitleX-ray structure of human acetylcholinesterase ternary complex with paraoxon and oxime MMB4 (POX-hAChE-MMB4)
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholine hydrolysis / oxime reactivator
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / positive regulation of protein secretion / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / nervous system development / amyloid-beta binding / cell adhesion / hydrolase activity / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / 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
Similarity search - Domain/homology
Chem-3VI / DIETHYL PHOSPHONATE / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKovalevsky, A.Y. / Gerlits, O. / Radic, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)U01NS083451 United States
CitationJournal: Structure / Year: 2022
Title: Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering.
Authors: Gerlits, O. / Fajer, M. / Cheng, X. / Blumenthal, D.K. / Radic, Z. / Kovalevsky, A.
History
DepositionJul 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)121,92112
Polymers120,5762
Non-polymers1,34510
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.503, 124.503, 129.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 60287.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#2: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H11O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3VI / 1,1'-methylenebis{4-[(E)-(hydroxyimino)methyl]pyridin-1-ium}


Mass: 258.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.79 Å3/Da / Density % sol: 74.33 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, pH 7.5, 100 mM KNO3 and 9 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 53935 / % possible obs: 97.7 % / Redundancy: 2.7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.87
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5473 / CC1/2: 0.551 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U34

6u34


Resolution: 2.8→38.863 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2778 5.22 %random
Rwork0.1918 ---
obs0.1933 53195 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→38.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8376 0 90 155 8621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028726
X-RAY DIFFRACTIONf_angle_d0.56611920
X-RAY DIFFRACTIONf_dihedral_angle_d15.7345102
X-RAY DIFFRACTIONf_chiral_restr0.0431256
X-RAY DIFFRACTIONf_plane_restr0.0051576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.84650.37861550.30212399X-RAY DIFFRACTION92
2.8465-2.89820.33961080.28932487X-RAY DIFFRACTION94
2.8982-2.9540.31061700.2622451X-RAY DIFFRACTION94
2.954-3.01420.31681250.24982452X-RAY DIFFRACTION95
3.0142-3.07970.31221330.25632477X-RAY DIFFRACTION94
3.0797-3.15140.32511110.24452379X-RAY DIFFRACTION91
3.1514-3.23010.30911560.24852524X-RAY DIFFRACTION98
3.2301-3.31740.24271420.23982602X-RAY DIFFRACTION99
3.3174-3.4150.23591430.23432565X-RAY DIFFRACTION99
3.415-3.52510.25921320.19892610X-RAY DIFFRACTION99
3.5251-3.6510.20631230.20062613X-RAY DIFFRACTION99
3.651-3.79710.22021460.192577X-RAY DIFFRACTION98
3.7971-3.96970.20311230.18032533X-RAY DIFFRACTION98
3.9697-4.17880.22741220.16592472X-RAY DIFFRACTION93
4.1788-4.44030.17991490.15522597X-RAY DIFFRACTION99
4.4403-4.78260.14791410.14832608X-RAY DIFFRACTION99
4.7826-5.26280.18511490.15852557X-RAY DIFFRACTION99
5.2628-6.02190.1851710.16982467X-RAY DIFFRACTION96
6.0219-7.57770.17221750.16462516X-RAY DIFFRACTION97
7.5777-38.860.1721040.15452531X-RAY DIFFRACTION95

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