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- PDB-8dt5: X-ray structure of human acetylcholinesterase ternary complex wit... -

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Basic information

Entry
Database: PDB / ID: 8dt5
TitleX-ray structure of human acetylcholinesterase ternary complex with paraoxon and oxime RS170B (POX-hAChE-RS170B)
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholine hydrolysis / oxime reactivator
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / side of membrane / collagen binding / synapse assembly / laminin binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / retina development in camera-type eye / cell adhesion / hydrolase activity / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleus / membrane / 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
DIETHYL PHOSPHONATE / Chem-LND / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.3Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,23015
Polymers120,5762
Non-polymers1,65413
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.700, 124.700, 129.186
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LND / 4-carbamoyl-1-(3-{2-[(E)-(hydroxyimino)methyl]-1H-imidazol-1-yl}propyl)pyridin-1-ium


Mass: 274.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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

Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 20 mM sodium citrate, and 7-8.5 % PEG6000

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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: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 66518 / % possible obs: 95.4 % / Redundancy: 2.6 % / CC1/2: 0.971 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2 / Num. unique obs: 6738 / CC1/2: 0.475 / % possible all: 96.2

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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: 2.6→38.921 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 23.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 3173 4.94 %random
Rwork0.1879 ---
obs0.1894 64293 92.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8376 0 110 254 8740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048755
X-RAY DIFFRACTIONf_angle_d0.69411956
X-RAY DIFFRACTIONf_dihedral_angle_d6.7286055
X-RAY DIFFRACTIONf_chiral_restr0.0461257
X-RAY DIFFRACTIONf_plane_restr0.0051579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6310.2698970.28411647X-RAY DIFFRACTION57
2.631-2.67210.3611230.2752244X-RAY DIFFRACTION79
2.6721-2.71590.30771330.26592530X-RAY DIFFRACTION88
2.7159-2.76270.32041580.26132683X-RAY DIFFRACTION93
2.7627-2.81290.32041320.26492695X-RAY DIFFRACTION94
2.8129-2.8670.30081370.25022716X-RAY DIFFRACTION95
2.867-2.92550.2711220.24092800X-RAY DIFFRACTION96
2.9255-2.98910.33411250.23132744X-RAY DIFFRACTION95
2.9891-3.05860.24121920.22342636X-RAY DIFFRACTION93
3.0586-3.1350.22971530.22412433X-RAY DIFFRACTION86
3.135-3.21980.25691210.22112868X-RAY DIFFRACTION98
3.2198-3.31450.24641400.22112795X-RAY DIFFRACTION98
3.3145-3.42140.28961410.22012776X-RAY DIFFRACTION97
3.4214-3.54360.22961430.20572863X-RAY DIFFRACTION97
3.5436-3.68540.26511090.19552770X-RAY DIFFRACTION96
3.6854-3.8530.21881440.18342754X-RAY DIFFRACTION96
3.853-4.05590.17841290.16712663X-RAY DIFFRACTION92
4.0559-4.30970.1611690.15752732X-RAY DIFFRACTION95
4.3097-4.6420.16291210.13842818X-RAY DIFFRACTION98
4.642-5.10820.17051340.13752833X-RAY DIFFRACTION98
5.1082-5.84520.17311390.16152745X-RAY DIFFRACTION95
5.8452-7.35620.20071650.16032704X-RAY DIFFRACTION95
7.3562-38.920.14911460.13982671X-RAY DIFFRACTION93

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