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- PDB-6wvo: Crystal Structure of Recombinant Human Acetylcholinesterase In Co... -

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Basic information

Entry
Database: PDB / ID: 6wvo
TitleCrystal Structure of Recombinant Human Acetylcholinesterase In Complex with GD and HI-6
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / nerve agent / acetylcholinesterase / tabun / GA
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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
(1R)-1,2,2-TRIMETHYLPROPYL (S)-METHYLPHOSPHINATE / Chem-HI6 / NITRATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,78014
Polymers118,8942
Non-polymers2,88612
Water9,278515
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.871, 104.871, 322.818
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

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Protein , 1 types, 2 molecules AB

#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

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Sugars , 2 types, 3 molecules

#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.: 2
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
#6: 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.: 1 / Source method: obtained synthetically / 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

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Non-polymers , 6 types, 524 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GD8 / (1R)-1,2,2-TRIMETHYLPROPYL (S)-METHYLPHOSPHINATE


Mass: 164.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17O2P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-HI6 / 4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM / 1-(2-HYDROXY-IMINOMETHYLPYRIDINIUM)-1-(4-CARBOXYAMINO)-PYRIDINIUM DIMETHYLETHER


Mass: 288.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N4O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#8: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H34O9
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O

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Details

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 % sol: 71.46 % / Mosaicity: 0.432 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, KNO3

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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: 2.193→200 Å / Num. obs: 106415 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 42.63 Å2 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.075 / Rrim(I) all: 0.23 / Χ2: 1.01 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.193-2.249.32.86152740.5490.9833.0280.545100
2.24-2.289.32.30652320.6280.7912.440.558100
2.28-2.329.42.10952280.7140.7242.2320.548100
2.32-2.379.31.89152480.7320.6522.0020.561100
2.37-2.429.31.67652460.770.5781.7750.569100
2.42-2.489.21.39852480.8190.4821.4810.588100
2.48-2.549.21.1752880.8320.4041.2390.602100
2.54-2.619.10.98152440.8760.341.0390.613100
2.61-2.699.10.80652830.9070.280.8540.654100
2.69-2.779.10.65553140.9330.2270.6940.694100
2.77-2.879.20.52752470.9480.1810.5580.768100
2.87-2.999.20.40253240.9730.1380.4260.865100
2.99-3.129.20.29752780.9830.1020.3141.036100
3.12-3.299.10.24953240.9840.0850.2631.186100
3.29-3.499.10.18653210.9890.0640.1971.437100
3.49-3.7690.15253600.9910.0520.1611.746100
3.76-4.1490.13153480.9930.0450.1392.121100
4.14-4.748.90.11854050.9920.0410.1252.396100
4.74-5.979.40.09454570.9950.0320.0991.637100
5.97-20010.30.05257460.9990.0170.0551.08499.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIX1.17.1-3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.19→49.87 Å / SU ML: 0.3233 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.6184 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 5306 5 %
Rwork0.1955 100849 -
obs0.1973 106155 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.88 Å2
Refinement stepCycle: LAST / Resolution: 2.19→49.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8320 0 193 515 9028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838917
X-RAY DIFFRACTIONf_angle_d1.00312194
X-RAY DIFFRACTIONf_chiral_restr0.05561297
X-RAY DIFFRACTIONf_plane_restr0.00741606
X-RAY DIFFRACTIONf_dihedral_angle_d4.24057044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.38091790.38093214X-RAY DIFFRACTION96.17
2.22-2.240.38441680.37233269X-RAY DIFFRACTION99.65
2.24-2.270.39051700.35973359X-RAY DIFFRACTION99.86
2.27-2.30.40291700.34053289X-RAY DIFFRACTION99.63
2.3-2.330.341760.32833370X-RAY DIFFRACTION99.55
2.33-2.360.3511880.31023245X-RAY DIFFRACTION99.51
2.36-2.40.34191650.30233328X-RAY DIFFRACTION99.8
2.4-2.430.3251730.28633343X-RAY DIFFRACTION99.69
2.43-2.470.31141830.26453280X-RAY DIFFRACTION99.71
2.47-2.510.26141940.25533322X-RAY DIFFRACTION99.94
2.51-2.550.33831650.25263386X-RAY DIFFRACTION99.97
2.55-2.60.27951730.25013303X-RAY DIFFRACTION99.89
2.6-2.650.27311900.23893303X-RAY DIFFRACTION99.83
2.65-2.70.2531800.22353360X-RAY DIFFRACTION99.83
2.7-2.760.29431650.21883383X-RAY DIFFRACTION99.92
2.76-2.830.28161990.21573312X-RAY DIFFRACTION99.89
2.83-2.90.28011560.21113341X-RAY DIFFRACTION99.86
2.9-2.980.2431770.20073386X-RAY DIFFRACTION99.89
2.98-3.060.22861720.19293326X-RAY DIFFRACTION99.91
3.06-3.160.21181760.19733369X-RAY DIFFRACTION99.92
3.16-3.280.24041640.20293396X-RAY DIFFRACTION99.97
3.28-3.410.22511880.18383357X-RAY DIFFRACTION99.97
3.41-3.560.22651800.17893373X-RAY DIFFRACTION99.97
3.56-3.750.20031820.17163391X-RAY DIFFRACTION100
3.75-3.990.18441720.15283373X-RAY DIFFRACTION99.89
3.99-4.290.1611690.14243417X-RAY DIFFRACTION100
4.29-4.720.17381900.13573425X-RAY DIFFRACTION99.97
4.72-5.410.16381590.14733481X-RAY DIFFRACTION100
5.41-6.810.24142060.17493463X-RAY DIFFRACTION100
6.81-49.870.21341770.18263685X-RAY DIFFRACTION99.66

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