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- PDB-7qyn: Mus musculus acetylcholinesterase in complex with 2-((hydroxyimin... -

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Basic information

Entry
Database: PDB / ID: 7qyn
TitleMus musculus acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Complex / Reactivator
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / 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
Chem-I1X / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsForsgren, N. / Lindgren, C. / Edvinsson, L. / Linusson, A. / Ekstrom, F.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Other government Sweden
Swedish Research Council Sweden
CitationJournal: Chemistry / Year: 2022
Title: Broad-Spectrum Antidote Discovery by Untangling the Reactivation Mechanism of Nerve-Agent-Inhibited Acetylcholinesterase.
Authors: Lindgren, C. / Forsgren, N. / Hoster, N. / Akfur, C. / Artursson, E. / Edvinsson, L. / Svensson, R. / Worek, F. / Ekstrom, F. / Linusson, A.
History
DepositionJan 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)123,13823
Polymers119,5292
Non-polymers3,60921
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint35 kcal/mol
Surface area38430 Å2
Unit cell
Length a, b, c (Å)78.595, 110.764, 227.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59764.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Plasmid: PCDNA3.1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase
#2: 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.: 4 / 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, 305 molecules

#3: Chemical ChemComp-I1X / 4-methyl-3-nitro-~{N}-[(2~{E},4~{E})-5-[2-[(oxidanylamino)methyl]pyridin-1-yl]penta-2,4-dienyl]benzamide


Mass: 371.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O4
#6: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 28-30 % (w/v) PEG750MME 0.1 M HEPES pH 6.9-7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 1.04088 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04088 Å / Relative weight: 1
ReflectionResolution: 2.5→29.5 Å / Num. obs: 69672 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 42.38 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 10058 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.5→28.6921 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 1396 2.01 %
Rwork0.1664 68067 -
obs0.1671 69463 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.99 Å2 / Biso mean: 51.88 Å2 / Biso min: 21.59 Å2
Refinement stepCycle: final / Resolution: 2.5→28.6921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8333 0 241 288 8862
Biso mean--82.46 48.21 -
Num. residues----1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078859
X-RAY DIFFRACTIONf_angle_d1.112054
X-RAY DIFFRACTIONf_chiral_restr0.0421292
X-RAY DIFFRACTIONf_plane_restr0.0061572
X-RAY DIFFRACTIONf_dihedral_angle_d17.5083242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58930.28181490.236466976846100
2.5893-2.69290.30991500.22567086858100
2.6929-2.81540.24541340.211967446878100
2.8154-2.96360.27451390.20467406879100
2.9636-3.14910.21951570.195367556912100
3.1491-3.39190.24351130.187267956908100
3.3919-3.73260.2081510.163868086959100
3.7326-4.27120.18181290.143268506979100
4.2712-5.37540.13791350.127769077042100
5.3754-28.69210.16921390.15347063720298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.53980.129-0.20581.3391-0.06053.0957-0.0152-0.1909-0.01560.17580.0089-0.02020.13190.00060.00680.3090.0051-0.0220.29190.04040.304230.79411.063829.0937
25.28381.94250.85822.03340.50433.5857-0.12310.203-0.2937-0.20140.0619-0.22310.23110.26850.0490.31230.09830.04470.25510.02620.311342.26649.761910.3101
31.5267-0.0455-0.22571.0746-0.34024.0634-0.02190.06510.0557-0.13540.05540.17530.0566-0.4694-0.0380.2535-0.029-0.04460.31850.00530.342718.662616.75976.5454
47.6979-0.92852.46539.4201-1.05675.402-0.2524-0.2576-0.68650.29560.16151.03690.5536-1.53330.19570.4107-0.22820.00650.64590.05010.51436.78331.167613.5914
54.9755-1.8453-4.82162.76172.90656.667-0.05270.0498-0.353-0.2721-0.08130.23560.26-0.08260.0850.41440.0004-0.15040.50160.01430.353617.47816.2596-1.1945
68.921-2.4251-2.51832.45420.50734.79640.12720.51060.0816-0.3084-0.16750.2787-0.2817-0.80660.00020.49340.0102-0.10230.5372-0.13560.4172-3.62576.3158-62.0337
71.2622-1.0421.53721.4924-0.76673.50430.12830.2224-0.2738-0.371-0.19090.09230.3238-0.25930.01140.4293-0.0077-0.0530.4972-0.09210.29617.15010.3718-61.7611
81.8333-0.1491-0.22922.05930.66373.09380.1940.2186-0.2066-0.0466-0.25070.31990.2885-0.49220.04330.3526-0.0341-0.04610.4235-0.10870.34731.05541.5872-48.6782
93.865-1.96970.35673.3772-0.53562.86270.11460.36390.0897-0.1445-0.0871-0.1096-0.33710.1211-0.03660.3683-0.0399-0.02750.3141-0.06020.273412.303711.5423-48.9488
101.2583-1.2153-0.47063.74253.54287.94660.05580.0892-0.19710.29730.0759-0.23180.7810.9238-0.10370.5140.1258-0.1320.5253-0.05540.48224.4497-9.0938-46.6936
114.5736-2.0405-2.18982.16981.6494.46250.26960.06870.65710.0718-0.0478-0.5788-0.64260.575-0.23090.3841-0.0668-0.07690.434-0.0370.454518.356914.3341-40.4084
126.45493.18660.82296.93980.19152.74990.4268-0.1425-0.5940.5146-0.1214-0.15660.81680.106-0.31240.74310.0266-0.05750.3359-0.0220.349214.2655-6.2416-21.9715
132.0641-0.10830.50812.7999-0.2423.80960.1559-0.1947-0.11110.2509-0.1250.24380.2105-0.4847-0.04960.3653-0.05530.03410.3732-0.11150.32010.7065.8656-29.4107
148.9405-1.2527-0.37314.7865-2.12456.23580.4106-0.3870.756-0.2632-0.25130.4796-0.4383-0.7148-0.12390.50860.0635-0.04460.4069-0.08430.4078-1.031822.4255-28.938
158.71340.23196.75961.71040.23785.36320.10860.3616-0.16580.2377-0.1083-0.0912-0.00920.2478-0.02060.5236-0.0610.01260.3450.0340.255813.182311.2749-21.789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:228)A1 - 228
2X-RAY DIFFRACTION2chain 'A' and (resseq 229:324)A229 - 324
3X-RAY DIFFRACTION3chain 'A' and (resseq 325:486)A325 - 486
4X-RAY DIFFRACTION4chain 'A' and (resseq 487:513)A487 - 513
5X-RAY DIFFRACTION5chain 'A' and (resseq 514:542)A514 - 542
6X-RAY DIFFRACTION6chain 'B' and (resseq 4:45)B4 - 45
7X-RAY DIFFRACTION7chain 'B' and (resseq 46:71)B46 - 71
8X-RAY DIFFRACTION8chain 'B' and (resseq 72:158)B72 - 158
9X-RAY DIFFRACTION9chain 'B' and (resseq 159:240)B159 - 240
10X-RAY DIFFRACTION10chain 'B' and (resseq 241:297)B241 - 297
11X-RAY DIFFRACTION11chain 'B' and (resseq 298:331)B298 - 331
12X-RAY DIFFRACTION12chain 'B' and (resseq 332:382)B332 - 382
13X-RAY DIFFRACTION13chain 'B' and (resseq 383:486)B383 - 486
14X-RAY DIFFRACTION14chain 'B' and (resseq 487:513)B487 - 513
15X-RAY DIFFRACTION15chain 'B' and (resseq 514:543)B514 - 543

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