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

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Basic information

Entry
Database: PDB / ID: 6wvc
TitleCrystal Structure of Recombinant Human Acetylcholinesterase Inhibited by GD
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 / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-7PE / Chem-UCY / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 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 1.2Oct 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 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9198
Polymers118,8942
Non-polymers2,0256
Water11,926662
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9198
Polymers118,8942
Non-polymers2,0256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area4120 Å2
ΔGint10 kcal/mol
Surface area38810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.142, 105.142, 323.698
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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-Glycam 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
[]{[(4+1)][b-D-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.: 1
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

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Non-polymers , 3 types, 665 molecules

#4: Chemical ChemComp-UCY / (1S)-2,2-dimethylcyclopentyl (R)-methylphosphinate / 2,2-dimethylcyclopentyl methylphosphinate


Mass: 176.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H17O2P
#5: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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 Matthews: 4.34 Å3/Da / Density % sol: 71.69 % / Mosaicity: 0.345 °
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: 2.599→50 Å / Num. obs: 65019 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 45.95 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.047 / Rrim(I) all: 0.126 / Χ2: 0.939 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.599-2.647.20.59431830.9280.2380.6410.616100
2.64-2.697.20.52532180.9350.2110.5670.65100
2.69-2.747.20.44531690.9510.1790.480.672100
2.74-2.87.20.41232100.9540.1660.4450.684100
2.8-2.867.20.35332270.9610.1420.3810.754100
2.86-2.937.20.30332110.9730.1220.3270.816100
2.93-37.20.25632090.9770.1030.2770.864100
3-3.087.20.22232040.9830.090.240.969100
3.08-3.177.20.19232180.9870.0770.2070.982100
3.17-3.287.20.17432220.9840.070.1881.052100
3.28-3.397.10.14632450.9910.0590.1581.117100
3.39-3.537.10.13532080.9880.0540.1451.245100
3.53-3.697.10.11932020.9910.0480.1281.159100
3.69-3.887.10.10832690.9930.0430.1161.175100
3.88-4.137.10.10232550.9930.0410.111.161100
4.13-4.4570.09932610.9910.040.1071.223100
4.45-4.8970.09932900.9910.040.1071.277100
4.89-5.66.90.09233150.9930.0370.0991.102100
5.6-7.056.70.07233690.9950.030.0780.761100
7.05-506.50.04835340.9970.020.0520.49499.7

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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: 2.599→46.415 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 3200 4.93 %
Rwork0.1554 61693 -
obs0.1575 64893 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.04 Å2 / Biso mean: 50.334 Å2 / Biso min: 27.42 Å2
Refinement stepCycle: final / Resolution: 2.599→46.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8343 0 131 662 9136
Biso mean--80.41 54.93 -
Num. residues----1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088778
X-RAY DIFFRACTIONf_angle_d1.0212007
X-RAY DIFFRACTIONf_chiral_restr0.0561292
X-RAY DIFFRACTIONf_plane_restr0.0081576
X-RAY DIFFRACTIONf_dihedral_angle_d14.175146
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5991-2.63790.26711260.2148262499
2.6379-2.67910.28491240.20152673100
2.6791-2.72310.23111340.19422616100
2.7231-2.770.2471330.19782674100
2.77-2.82040.27451570.18922578100
2.8204-2.87460.24171150.18252658100
2.8746-2.93330.22491550.18122667100
2.9333-2.9970.23551460.17032649100
2.997-3.06680.24331340.17562642100
3.0668-3.14340.21331470.1712636100
3.1434-3.22840.214990.17592687100
3.2284-3.32340.23521790.17412643100
3.3234-3.43060.19711240.16322676100
3.4306-3.55320.19381320.16372680100
3.5532-3.69540.20011370.15872683100
3.6954-3.86350.17951530.14282670100
3.8635-4.06710.20071230.13072710100
4.0671-4.32170.17171630.12552673100
4.3217-4.65510.13831370.11652697100
4.6551-5.1230.15311450.12192713100
5.123-5.86310.17511380.14532780100
5.8631-7.38210.20061330.16422767100
7.3821-46.4150.19261660.1641289799

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