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- PDB-6o66: Structure of VX-phosphonylated hAChE in complex with oxime reacti... -

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Basic information

Entry
Database: PDB / ID: 6o66
TitleStructure of VX-phosphonylated hAChE in complex with oxime reactivator RS-170B
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / human acetylcholinesterase / VX-phosphonylated / VX-hAChE / oxime reactivator / imidazole-based oxime / RS-170B
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 / hydrolase activity / cell adhesion / 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
Chem-LND / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.452 Å
AuthorsGerlits, O. / Kovalevsky, A. / Radic, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1U01NS083451 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Productive reorientation of a bound oxime reactivator revealed in room temperature X-ray structures of native and VX-inhibited human acetylcholinesterase.
Authors: Gerlits, O. / Kong, X. / Cheng, X. / Wymore, T. / Blumenthal, D.K. / Taylor, P. / Radic, Z. / Kovalevsky, A.
History
DepositionMar 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,25814
Polymers120,7882
Non-polymers1,47012
Water4,161231
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,25814
Polymers120,7882
Non-polymers1,47012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_674-x+y+1,-x+2,z-1/31
Buried area4570 Å2
ΔGint-22 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.375, 124.375, 129.304
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: 60394.031 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-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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 4.85 Å3/Da / Density % sol: 74.63 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 10 mM sodium citrate, 100 mM HEPES, pH 7, and 6-8 % 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: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. obs: 73508 / % possible obs: 93.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.1
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.585 / Num. unique obs: 7714

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.452→38.832 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.25
RfactorNum. reflection% reflection
Rfree0.2289 3677 5 %
Rwork0.2066 --
obs0.2077 73508 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.452→38.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8388 0 100 231 8719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028756
X-RAY DIFFRACTIONf_angle_d0.52111956
X-RAY DIFFRACTIONf_dihedral_angle_d13.0965120
X-RAY DIFFRACTIONf_chiral_restr0.0421257
X-RAY DIFFRACTIONf_plane_restr0.0051579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4519-2.48420.33481090.30272263X-RAY DIFFRACTION75
2.4842-2.51820.31411170.28472322X-RAY DIFFRACTION78
2.5182-2.55410.28271120.28122425X-RAY DIFFRACTION80
2.5541-2.59230.2961230.28422503X-RAY DIFFRACTION82
2.5923-2.63280.34681390.28472317X-RAY DIFFRACTION78
2.6328-2.67590.33561130.27152313X-RAY DIFFRACTION77
2.6759-2.7220.29831300.27982651X-RAY DIFFRACTION88
2.722-2.77150.29641630.27522745X-RAY DIFFRACTION93
2.7715-2.82480.33771340.27482831X-RAY DIFFRACTION93
2.8248-2.88250.31841560.26082789X-RAY DIFFRACTION94
2.8825-2.94510.30461230.25992842X-RAY DIFFRACTION94
2.9451-3.01360.27181500.25252823X-RAY DIFFRACTION94
3.0136-3.08890.26971340.24252849X-RAY DIFFRACTION94
3.0889-3.17240.27561540.24522811X-RAY DIFFRACTION94
3.1724-3.26570.25091430.23732826X-RAY DIFFRACTION93
3.2657-3.37110.27421450.24042725X-RAY DIFFRACTION92
3.3711-3.49150.2531210.21812543X-RAY DIFFRACTION85
3.4915-3.63120.21461530.20942855X-RAY DIFFRACTION96
3.6312-3.79630.22531640.20012893X-RAY DIFFRACTION97
3.7963-3.99630.21831530.17952891X-RAY DIFFRACTION96
3.9963-4.24640.16891560.16832841X-RAY DIFFRACTION96
4.2464-4.57380.16971620.15342827X-RAY DIFFRACTION94
4.5738-5.03320.17591650.15262671X-RAY DIFFRACTION90
5.0332-5.75940.2051370.16732756X-RAY DIFFRACTION92
5.7594-7.24860.18211720.16622854X-RAY DIFFRACTION96
7.2486-38.83690.16421490.14472665X-RAY DIFFRACTION89

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