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- PDB-7e3d: Crystal structure of human acetylcholinesterase -

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Basic information

Entry
Database: PDB / ID: 7e3d
TitleCrystal structure of human acetylcholinesterase
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Human acetylcholinesterase / hAChE / Alzheimer's disease
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 / hydrolase activity / cell adhesion / 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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDileep, K.V. / Ihara, K. / Mishima-Tsumagari, C. / Kukimoto-Niino, M. / Yonemochi, M. / Hanada, K. / Shirouzu, M. / Zhang, K.Y.J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Crystal structure of human acetylcholinesterase in complex with tacrine: Implications for drug discovery
Authors: Dileep, K. / Ihara, K. / Mishima-Tsumagari, C. / Kukimoto-Niino, M. / Yonemochi, M. / Hanada, K. / Shirouzu, M. / Zhang, K.Y.
History
DepositionFeb 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 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)119,9775
Polymers118,4662
Non-polymers1,5123
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint12 kcal/mol
Surface area38450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.931, 104.931, 322.566
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 17 or resid 19...
21(chain B and ((resid 4 and (name N or name...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLULEULEU(chain A and (resid 4 through 17 or resid 19...AA4 - 171 - 14
121GLYGLYLYSLYS(chain A and (resid 4 through 17 or resid 19...AA19 - 5316 - 50
131GLUGLUALAALA(chain A and (resid 4 through 17 or resid 19...AA4 - 5421 - 539
141GLUGLUGLUGLU(chain A and (resid 4 through 17 or resid 19...AA8178
151GLUGLUALAALA(chain A and (resid 4 through 17 or resid 19...AA4 - 5421 - 539
161GLUGLUALAALA(chain A and (resid 4 through 17 or resid 19...AA4 - 5421 - 539
171GLUGLUALAALA(chain A and (resid 4 through 17 or resid 19...AA4 - 5421 - 539
181GLUGLUALAALA(chain A and (resid 4 through 17 or resid 19...AA4 - 5421 - 539
191GLUGLUALAALA(chain A and (resid 4 through 17 or resid 19...AA4 - 5421 - 539
211GLUGLUGLUGLU(chain B and ((resid 4 and (name N or name...BB41
221GLUGLUALAALA(chain B and ((resid 4 and (name N or name...BB4 - 5421 - 539
231GLUGLUALAALA(chain B and ((resid 4 and (name N or name...BB4 - 5421 - 539
241GLUGLUALAALA(chain B and ((resid 4 and (name N or name...BB4 - 5421 - 539
251GLUGLUALAALA(chain B and ((resid 4 and (name N or name...BB4 - 5421 - 539
112NAGNAGFUCFUCchain CCC1 - 3
212NAGNAGFUCFUCchain DDD1 - 3

NCS ensembles :
ID
1
2

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 59232.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#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: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.33 Å3/Da / Density % sol: 71.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Tris HCl buffer pH 9.0, 20 % PEG 3350, 200 mM KNO3
PH range: 8.0 - 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.15 Å / Num. obs: 71274 / % possible obs: 98.5 % / Redundancy: 4.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.9 / Num. measured all: 327664
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.5-2.564.10.7031764843250.739295
11.99-47.153.90.03730237700.99826.498.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
PHASER1.17.1-3600phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.5→47.15 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 3452 4.85 %
Rwork0.2029 67714 -
obs0.2048 71166 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.26 Å2 / Biso mean: 36.7428 Å2 / Biso min: 12.97 Å2
Refinement stepCycle: final / Resolution: 2.5→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 0 101 108 8459
Biso mean--75.59 33.03 -
Num. residues----1065
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3158X-RAY DIFFRACTION3.327TORSIONAL
12B3158X-RAY DIFFRACTION3.327TORSIONAL
21C42X-RAY DIFFRACTION3.327TORSIONAL
22D42X-RAY DIFFRACTION3.327TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.530.32191200.27872571269196
2.53-2.570.33281270.26852504263192
2.57-2.610.36621620.26262518268094
2.61-2.650.31071070.250527032810100
2.65-2.690.26171840.245827252909100
2.69-2.740.27511660.243626242790100
2.74-2.790.27021260.247227542880100
2.79-2.840.29351600.239627282888100
2.84-2.90.27031370.23926862823100
2.9-2.960.32611240.240627082832100
2.96-3.030.28971330.23727642897100
3.03-3.110.31761300.231827302860100
3.11-3.190.29621310.223727582889100
3.19-3.290.26021380.221927152853100
3.29-3.390.28761170.207827802897100
3.39-3.510.2411290.22127292858100
3.51-3.650.25451260.216227502876100
3.65-3.820.2211260.186627472873100
3.82-4.020.19311550.17682767292299
4.02-4.270.17111530.16512675282899
4.27-4.60.19831570.15322649280696
4.6-5.070.2091310.15182480261188
5.07-5.80.17441090.180928362945100
5.8-7.30.22711560.193628182974100
7.3-47.150.23211480.18552995314399

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