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- PDB-6wuv: Crystal Structure of Recombinant Human Acetylcholinesterase Inhib... -

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Basic information

Entry
Database: PDB / ID: 6wuv
TitleCrystal Structure of Recombinant Human Acetylcholinesterase Inhibited by GA
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / nerve agent / acetylcholinesterase / tabun / GA
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
ethoxy-~{N},~{N}-dimethyl-phosphonamidic acid / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsMcGuire, J.R. / Bester, S.M. / Pegan, S.D. / Height, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)CB#3889 United States
CitationJournal: Chem.Res.Toxicol. / Year: 2021
Title: Structural and Biochemical Insights into the Inhibition of Human Acetylcholinesterase by G-Series Nerve Agents and Subsequent Reactivation by HI-6.
Authors: McGuire, J.R. / Bester, S.M. / Guelta, M.A. / Cheung, J. / Langley, C. / Winemiller, M.D. / Bae, S.Y. / Funk, V. / Myslinski, J.M. / Pegan, S.D. / Height, J.J.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 2, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Oct 18, 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 1.4Oct 16, 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)121,57610
Polymers118,8942
Non-polymers2,6818
Water4,846269
1
B: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,57610
Polymers118,8942
Non-polymers2,6818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area4820 Å2
ΔGint31 kcal/mol
Surface area38960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.495, 104.495, 323.839
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 59447.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: 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.: 3
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
#4: Chemical ChemComp-ELT / ethoxy-~{N},~{N}-dimethyl-phosphonamidic acid


Mass: 153.117 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 4.39 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-21% Polyethylene glycol 3350 (PEG), 0.17 - 0.21M Potassium Nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 61490 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 63.87 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.06 / Rrim(I) all: 0.115 / Χ2: 1.078 / Net I/σ(I): 11.1 / Num. measured all: 219753
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.63-2.683.40.74730560.6610.4760.8881.00999
2.68-2.723.60.64529770.710.3960.7580.87399
2.72-2.783.60.55729980.7710.3420.6550.89499.1
2.78-2.833.60.4630620.8170.2810.540.96299.2
2.83-2.893.60.37530330.8870.2280.440.99899.2
2.89-2.963.60.3230140.9190.1940.3751.03899.2
2.96-3.043.60.25930350.940.1570.3031.14299.2
3.04-3.123.60.21930290.9640.1330.2571.30499.3
3.12-3.213.70.18330400.9650.110.2141.24899.4
3.21-3.313.60.15530350.9740.0950.1821.2799.4
3.31-3.433.60.13330570.9780.0810.1561.35299.4
3.43-3.573.60.11830800.9830.0720.1391.25399.5
3.57-3.733.60.11530790.9780.070.1351.31499.5
3.73-3.933.60.09830510.9810.060.1151.08399.4
3.93-4.173.60.08431060.9880.0510.0981.11899.4
4.17-4.53.60.07930790.9870.0480.0931.00199.4
4.5-4.953.60.07931280.9880.0470.0920.98899.5
4.95-5.663.60.08531220.9840.0510.0990.91199.6
5.66-7.133.50.06731890.990.040.0780.90899.7
7.13-503.30.07133200.9820.0450.0840.85398

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
PHENIX1.17.1-3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.63→41.192 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 3056 4.97 %
Rwork0.1702 58398 -
obs0.172 61454 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.67 Å2 / Biso mean: 66.6837 Å2 / Biso min: 32.71 Å2
Refinement stepCycle: final / Resolution: 2.63→41.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8267 0 172 269 8708
Biso mean--117.72 67.68 -
Num. residues----1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078826
X-RAY DIFFRACTIONf_angle_d1.03512098
X-RAY DIFFRACTIONf_chiral_restr0.0731318
X-RAY DIFFRACTIONf_plane_restr0.0071585
X-RAY DIFFRACTIONf_dihedral_angle_d5.9866994
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.63-2.67070.33431280.2547243891
2.6707-2.71450.27861560.2449258399
2.7145-2.76130.2671310.2234260299
2.7613-2.81150.26941670.2197261599
2.8115-2.86550.22921280.2186258699
2.8655-2.9240.28811370.2119266399
2.924-2.98760.23131350.1991263999
2.9876-3.0570.24941350.191260799
3.057-3.13350.20531330.1876263099
3.1335-3.21820.27431160.1805266599
3.2182-3.31280.18951550.1829262999
3.3128-3.41970.20811470.1792262999
3.4197-3.54180.21341330.179266899
3.5418-3.68360.21911220.16842669100
3.6836-3.85110.18811270.15532687100
3.8511-4.0540.20811210.1489268199
4.054-4.30770.19351450.14472665100
4.3077-4.63990.18811530.1335267699
4.6399-5.10610.15971500.13842692100
5.1061-5.84310.18721450.16262741100
5.8431-7.35490.20951440.18632758100
7.3549-41.1920.19481480.1762287598

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