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- PDB-7r4e: RVX-inhibited acetylcholinesterase in complex with 2-((hydroxyimi... -

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Basic information

Entry
Database: PDB / ID: 7r4e
TitleRVX-inhibited acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Ternary 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: 3.00001172335 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
DepositionFeb 8, 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

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,81517
Polymers119,7972
Non-polymers3,01715
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.956, 110.997, 227.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59898.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RVX phosphylation product covalently attached to Ser203
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Plasmid: PCDNA3.1 / Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase
#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.: 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 , 5 types, 132 molecules

#2: 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.: 5 / 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.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 4.16 Å3/Da / Density % sol: 70.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 27-30 % (w/v) PEG750MME 0.1 M HEPES pH 7.0-7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→29.1068766315 Å / Num. obs: 40881 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 50.2675654632 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 16.8
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 5910

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 3.00001172335→29.1068766315 Å / SU ML: 0.315484156577 / Cross valid method: FREE R-VALUE / σ(F): 1.33545909431 / Phase error: 22.7870375303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205342294478 793 1.94854657591 %
Rwork0.164257687136 39904 -
obs0.165054865654 40697 99.6205816117 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.4455610376 Å2
Refinement stepCycle: LAST / Resolution: 3.00001172335→29.1068766315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8345 0 179 121 8645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008910871213588837
X-RAY DIFFRACTIONf_angle_d1.0440541620412057
X-RAY DIFFRACTIONf_chiral_restr0.05678245324221289
X-RAY DIFFRACTIONf_plane_restr0.007260301012751576
X-RAY DIFFRACTIONf_dihedral_angle_d12.5531293627088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.00001172335-3.18780.2949493471891440.2230265107276519X-RAY DIFFRACTION99.2699642431
3.1878-3.43350.2652687447451150.2030899024936571X-RAY DIFFRACTION99.7166293811
3.4335-3.77840.2267480205951420.1748416627896578X-RAY DIFFRACTION99.481865285
3.7784-4.32360.1990648138981250.1470458044896595X-RAY DIFFRACTION99.703264095
4.3236-5.44150.1467962645321320.1346201191026702X-RAY DIFFRACTION99.8830751242
5.4415-29.10687663150.1898713106541350.1588591770636939X-RAY DIFFRACTION99.661876585
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)
12.033627159560.477788915944-1.073882972071.73180623389-0.2572661186775.72245648465-0.563717433454-0.6587205231970.3418350135250.6551685634640.3735634907080.0606614289735-0.175081380523-0.398997621212-0.02700990711850.5794900222220.005293303717360.0443854575360.5447516065550.003675157682220.33577801713625.633260191913.603558785144.2822780503
23.5245118750.226212415601-0.433568008272.06392741542-0.5621432973365.34751083754-0.156027985367-0.2157589167640.2342406670720.1685733969930.111216864759-0.025668725675-0.003530577072960.1141114424420.01788123441980.3216098293650.00122046811336-0.02581872859110.3459115796120.01427514446640.21441948786732.160899824315.325896677127.9660824251
34.164443017060.952343347615-0.2027560836661.65340661228-0.5406393859535.35102822255-0.112277471278-0.105455265086-0.4225356498250.06416197577310.0917599520166-0.1457344464810.567903000645-0.009541124548320.05484304827360.4119623559120.0536070924177-0.01638574668670.2244658562680.02708919179970.29185577886132.12990612833.0860438218421.1794222769
44.320204400841.910690810.6047624885961.720117344940.4325157357624.70165935593-0.405966612480.8687624368570.289008904653-0.305192591190.164518200497-0.286564883765-0.2766368329670.7642705000240.1464907239190.4078712642020.03953736222440.01506791933470.6275126908990.09050124137440.35792612452248.940474103316.201722686210.5694592041
56.49912512014-0.523962677030.6025593581650.4547560743430.2432649006224.44855122455-0.03553984986870.298491951994-1.12838012065-0.2907191973440.03415736073030.2070418423970.8753642149420.4627528752280.03607818889530.624352183674-0.03040422088720.04695768497580.3356007839540.009017739977060.45665447168130.9285613771-0.97657471989211.1923306693
63.13883739876-1.68764648486-1.918021108998.53414332462.804318802114.006353109330.1655989070010.1268246057870.18102402954-0.6089653589170.072926620249-0.176820001786-0.3102502421890.117234631174-0.2143009443420.333820189297-0.0320674138788-0.06133210039380.4805509464550.08864992271870.27587922999926.432114067321.7320668117-3.98388937724
71.28990495566-0.1601133367240.1011523176992.40252602755-0.4247924373774.031330340180.09587519576850.227775769702-0.0501629445046-0.2202151519850.04165450649170.2189532734150.254587817645-0.273735772634-0.139260892470.264395708066-0.0731328133426-0.05954079994450.495971343495-0.02073039614130.30556680440418.293435667213.8840709282.4931136016
81.37487104342-0.02259299234060.4942803352513.05494335318-1.096141282044.46703737965-0.0554103886822-0.1879237729090.0162623399260.05269622882050.1147808238570.450775904119-0.063194966342-0.994884045264-0.1560878303980.3214377879060.0235118011648-0.002189164483630.661869419440.03921336652890.36357282468212.368199493816.950423496120.5949247389
95.07900012893-1.100917915382.801328019158.02600183463-0.7381449273454.40100756437-0.009331513259920.111208666451-0.715772339273-0.1142067470820.1620855515590.9038783049870.512883367682-1.602578823110.07693576315390.408960367664-0.247287437587-0.03604299734390.7449801929840.02607656429160.5313565501157.162409577851.1601080430513.5059795861
100.923221537657-0.346485420483-2.547282770563.110059736093.172399470519.398786859070.1151668209860.184495015823-0.139073474157-0.45750103776-0.1758248889620.1679991827760.214902527988-0.3925395257120.05404301392790.5557098412740.0207686045339-0.1833798861320.7385662300810.03482535883920.34031019246918.2528447636.19974376077-1.54073906366
114.42706403972-1.14197755271-1.531206089871.337337293430.01055489688394.192029665630.1867652198930.858754058548-0.163765753895-0.126419068025-0.1952336432020.360769164244-0.218358298909-0.786018906669-0.03322665038450.475210013650.0155947214146-0.09485032997960.725995669376-0.1624764911940.374898587109-2.843035479845.97406823389-61.9761563219
121.4567258546-0.1076947765310.2742309356292.408756575610.6871540285164.204062862430.06244296603470.242984524648-0.2071539260140.0740457236652-0.2166941823760.2603004775080.437965920525-0.3266355780910.1004639965810.409307941012-0.0460521007549-0.06003485316480.579790409367-0.101300434480.3067446239342.689621928531.22148088259-51.6549854177
132.73280487049-1.902169362490.1669659143264.105986539350.5346728993613.148960422920.1432277956540.0705005831736-0.09848968476610.05034111017570.032014779845-0.3129728642420.2923028342710.514153612518-0.1521991657970.4096509779250.00781867698513-0.05656388668480.608715623901-0.0763141604650.29239514831817.50081667342.94525686315-47.987170307
142.00173707026-0.737355676378-0.05232147542161.878395693410.01215533812432.859739516720.314523122460.1067669694740.1521164988020.0796879927458-0.178680052366-0.178828883879-0.1071539995710.480037120537-0.1207555268520.408196089577-0.0621428492906-0.1145634185550.651863950316-0.07733637668970.37844671431615.245865474810.6259864731-37.0414160622
156.256860177662.426757496081.885359484154.558118521530.2582674508472.835285920370.415126496405-0.667353689681-0.4022479911110.325168426069-0.123114354287-0.09026882882510.649051121964-0.21057953551-0.3301199393240.82789938987-0.0352280507555-0.1273545943520.4552677322790.02613213653930.33951517854214.3653259381-5.29151766901-18.3441880406
162.745390334730.874775211929-0.2101023755713.6695240559-0.4860403189614.291390203240.158709612039-0.1108587032230.04018626289970.0393333356837-0.1007858060310.4064468342360.272221479164-0.673032546278-0.06517831064310.4176292063050.009934612321190.00918633530150.531469747571-0.1408774900250.302821746423-2.193127465138.39386980734-33.4673527785
175.03616086493-0.03309906295642.433853568617.24805595186-2.178110690849.098095632330.511485880243-0.2789137898050.539508924565-0.0252708381672-0.07577001870930.557538436987-0.160713112978-0.450590531443-0.4400974414210.4548851262580.02305514434060.02138421009960.374888458546-0.05519996997020.333129508455-0.78302380877922.3711289295-28.9013513717
185.16435789397-0.3300387449364.146346661991.55663586845-0.4912464159863.35025661514-0.1599173136480.125411611063-0.08717206057850.230885296069-0.0819770439056-0.08961598534020.329742906270.370188614280.2735734103580.625243193137-0.02065721866320.02782628073990.745035746264-0.02743340216550.24985941503212.848062932111.5853799562-21.7175070776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 240 )
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 297 )
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 331 )
6X-RAY DIFFRACTION6chain 'A' and (resid 332 through 382 )
7X-RAY DIFFRACTION7chain 'A' and (resid 383 through 440 )
8X-RAY DIFFRACTION8chain 'A' and (resid 441 through 486 )
9X-RAY DIFFRACTION9chain 'A' and (resid 487 through 513 )
10X-RAY DIFFRACTION10chain 'A' and (resid 514 through 543 )
11X-RAY DIFFRACTION11chain 'B' and (resid 4 through 45 )
12X-RAY DIFFRACTION12chain 'B' and (resid 46 through 158 )
13X-RAY DIFFRACTION13chain 'B' and (resid 159 through 300 )
14X-RAY DIFFRACTION14chain 'B' and (resid 301 through 341 )
15X-RAY DIFFRACTION15chain 'B' and (resid 342 through 406 )
16X-RAY DIFFRACTION16chain 'B' and (resid 407 through 486 )
17X-RAY DIFFRACTION17chain 'B' and (resid 487 through 513 )
18X-RAY DIFFRACTION18chain 'B' and (resid 514 through 542 )

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