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- PDB-2x8b: Crystal structure of human acetylcholinesterase inhibited by aged... -

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Basic information

Entry
Database: PDB / ID: 2x8b
TitleCrystal structure of human acetylcholinesterase inhibited by aged tabun and complexed with fasciculin-II
Components
  • ACETHYLCHOLINESTERASE
  • FASCICULIN-2
KeywordsHYDROLASE/TOXIN / HYDROLASE-TOXIN COMPLEX / CELL JUNCTION / HYDROLASE / GPI-ANCHOR / NEUROTRANSMITTER DEGRADATION / TABUN / AGING / SERINE ESTERASE / BLOOD GROUP ANTIGEN
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / choline metabolic process / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / laminin binding / side of membrane / synaptic cleft / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / toxin activity / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane
Similarity search - Function
Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Snake toxin-like superfamily / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. ...Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Snake toxin-like superfamily / 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 / Ribbon / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Fasciculin-2 / Acetylcholinesterase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
DENDROASPIS ANGUSTICEPS (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCarletti, E. / Colletier, J.P. / Nachon, F.
CitationJournal: J. Med. Chem. / Year: 2010
Title: Structural evidence that human acetylcholinesterase inhibited by tabun ages through O-dealkylation.
Authors: Carletti, E. / Colletier, J.P. / Dupeux, F. / Trovaslet, M. / Masson, P. / Nachon, F.
History
DepositionMar 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_assembly.oligomeric_count ..._chem_comp.pdbx_synonyms / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.6Dec 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETHYLCHOLINESTERASE
B: FASCICULIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,44619
Polymers71,5182
Non-polymers92817
Water4,252236
1
A: ACETHYLCHOLINESTERASE
B: FASCICULIN-2
hetero molecules

A: ACETHYLCHOLINESTERASE
B: FASCICULIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,89238
Polymers143,0354
Non-polymers1,85734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-11
Buried area9850 Å2
ΔGint-157 kcal/mol
Surface area43600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.310, 151.310, 247.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ACETHYLCHOLINESTERASE / ACHE


Mass: 64748.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: S203 IS PHOSPHORAMIDYLATED / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGS / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P22303, acetylcholinesterase
#2: Protein FASCICULIN-2 / / FASCICULIN-II / ACETYLCHOLINESTERASE TOXIN F-VII / TOXIN TA1 / FAS-2 / FAS2 / FAS-II


Mass: 6768.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) DENDROASPIS ANGUSTICEPS (eastern green mamba)
References: UniProt: P0C1Z0

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Sugars , 1 types, 2 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 4 types, 251 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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: 3.95 Å3/Da / Density % sol: 68.8 % / Description: NONE
Crystal growpH: 7.4 / Details: 0.1 M HEPES BUFFER PH 7.4, 1.3 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 22948 / % possible obs: 98.2 % / Observed criterion σ(I): 3.51 / Redundancy: 7 % / Biso Wilson estimate: 61.34 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 3.5
Reflection shellResolution: 2.95→3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 3.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
XDSdata reduction
XSCALEdata scaling
XDSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FSS

1fss


Resolution: 2.95→46.264 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1145 5 %RANDOM
Rwork0.1832 ---
obs0.1867 22941 98.82 %-
Solvent computationShrinkage radii: 0.9 Å
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-17.4 Å20 Å20 Å2
2--17.4 Å20 Å2
3----34.8 Å2
Refinement stepCycle: LAST / Resolution: 2.95→46.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4647 0 47 236 4930

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