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- PDB-8aen: Human acetylcholinesterase in complex with zinc and N,N,N-trimeth... -

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Basic information

Entry
Database: PDB / ID: 8aen
TitleHuman acetylcholinesterase in complex with zinc and N,N,N-trimethyl-2-oxo-2-(2-(pyridin-2-ylmethylene)hydrazineyl)ethan-1-aminium
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Inhibitor / complex / zinc / acetylcholinesterase
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 ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LWL / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsNachon, F. / Dias, J. / Brazzolotto, X.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-4210 France
CitationJournal: Chembiochem / Year: 2022
Title: Grid-Type Quaternary Metallosupramolecular Compounds Inhibit Human Cholinesterases through Dynamic Multivalent Interactions.
Authors: Nachon, F. / Brazzolotto, X. / Dias, J. / Courageux, C. / Drozdz, W. / Cao, X.Y. / Stefankiewicz, A.R. / Lehn, J.M.
History
DepositionJul 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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)125,68281
Polymers119,1522
Non-polymers6,53079
Water2,450136
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)210.850, 210.850, 114.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59576.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22303, acetylcholinesterase

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Sugars , 3 types, 4 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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 211 molecules

#5: Chemical ChemComp-LWL / N,N,N-trimethyl-2-oxo-2-(2-(pyridin-2-ylmethylene)hydrazineyl)ethan-1-aminium / ~{N}-[(~{E})-pyridin-2-ylmethylideneamino]-2-(trimethyl-$l^{4}-azanyl)ethanamide


Mass: 221.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N4O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#8: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 6.22 Å3/Da / Density % sol: 80.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.5 M LISO4, 100 MM HEPES PH7, 60 MM MGSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.980004 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980004 Å / Relative weight: 1
ReflectionResolution: 3.01→91.3 Å / Num. obs: 57675 / % possible obs: 99.74 % / Redundancy: 4.6 % / Biso Wilson estimate: 78.63 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.04067 / Rrim(I) all: 0.08822 / Net I/σ(I): 13.64
Reflection shellResolution: 3.01→3.118 Å / Rmerge(I) obs: 0.6037 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5746 / CC1/2: 0.865 / Rpim(I) all: 0.3098 / Rrim(I) all: 0.6798

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.20.1_4487refinement
Cootmodel building
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZWE

6zwe


Resolution: 3.01→91.3 Å / SU ML: 0.333 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1964 2831 4.91 %
Rwork0.1623 54844 -
obs0.1639 57675 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.43 Å2
Refinement stepCycle: LAST / Resolution: 3.01→91.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8311 0 339 136 8786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018841
X-RAY DIFFRACTIONf_angle_d1.124712100
X-RAY DIFFRACTIONf_chiral_restr0.05971305
X-RAY DIFFRACTIONf_plane_restr0.01051570
X-RAY DIFFRACTIONf_dihedral_angle_d7.81871259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.060.3621490.29422749X-RAY DIFFRACTION99.93
3.06-3.110.32791550.27612725X-RAY DIFFRACTION99.93
3.11-3.170.27651350.24252692X-RAY DIFFRACTION99.86
3.17-3.240.29641830.23992712X-RAY DIFFRACTION99.86
3.24-3.310.28541400.23952705X-RAY DIFFRACTION99.86
3.31-3.390.2281180.23362773X-RAY DIFFRACTION99.69
3.39-3.470.20621160.19642742X-RAY DIFFRACTION99.69
3.47-3.570.23121680.17922683X-RAY DIFFRACTION99.65
3.57-3.670.24231380.1682742X-RAY DIFFRACTION99.65
3.67-3.790.20981470.1522732X-RAY DIFFRACTION99.93
3.79-3.920.1671200.15322773X-RAY DIFFRACTION99.9
3.92-4.080.18061470.14692734X-RAY DIFFRACTION100
4.08-4.270.17441400.13792730X-RAY DIFFRACTION99.9
4.27-4.490.13931440.11992738X-RAY DIFFRACTION99.38
4.49-4.770.14831560.11532729X-RAY DIFFRACTION99.59
4.77-5.140.15421300.12612766X-RAY DIFFRACTION99.86
5.14-5.660.17761240.15072746X-RAY DIFFRACTION99.86
5.66-6.480.17571550.16852776X-RAY DIFFRACTION99.76
6.48-8.160.19591470.15932758X-RAY DIFFRACTION99.62
8.16-91.30.20341190.15722839X-RAY DIFFRACTION99.03
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)
12.7420836829-0.846998311633-0.6400392528731.813654491740.424025748091.29758350643-0.0907595309531-0.0570708174982-0.1118110931060.0560792469460.0144253402808-0.276578260151-0.00516317184221-0.05678801028720.0771824823570.456096975839-0.0466367810318-0.07076193010630.5373001499590.003274604697240.484600110368-191.730607375-88.39872035469.72171336467
22.804714575350.0852043736819-0.6389624932822.469240801130.09629103354772.072545212560.0424547349843-0.1340274571660.20942348135-0.09345089671230.0535722109062-0.444758934855-0.03165779915980.294167703596-0.09717607634740.405176774732-0.04189692175520.03637205096540.5763555879850.0571579652720.525613804502-155.684505823-122.480462056-23.0072206532
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain AAA - K5 - 607
22chain BBL - Q5 - 602

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