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- PDB-2ha3: Crystal structure of mouse acetylcholinesterase complexed with choline -

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Basic information

Entry
Database: PDB / ID: 2ha3
TitleCrystal structure of mouse acetylcholinesterase complexed with choline
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / HYDROLASE FOLD / SERINE ESTERASE / ACETYLCHOLINESTERASE / HOMODIMER / GLYCOSYLATED PROTEIN
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 / presynaptic membrane / nuclear envelope / 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, catalytic domain ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CHOLINE ION / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsBourne, Y. / Radic, Z. / Sulzenbacher, G. / Kim, E. / Taylor, P. / Marchot, P.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Substrate and product trafficking through the active center gorge of acetylcholinesterase analyzed by crystallography and equilibrium binding
Authors: Bourne, Y. / Radic, Z. / Sulzenbacher, G. / Kim, E. / Taylor, P. / Marchot, P.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,03810
Polymers119,5292
Non-polymers1,5098
Water13,367742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.387, 111.874, 227.147
Angle α, β, γ (deg.)89.97, 90.02, 90.04
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59764.488 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS (HEK) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / Variant (production host): LAMBDA ZAP / References: UniProt: P21836, acetylcholinesterase

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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.: 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 , 3 types, 747 molecules

#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H14NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / 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: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25-32% PEG550 MME or PEG600, 60-100mM HEPES or Na acetate, pH 6.5-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 92590 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.9
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.372 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 1845 2 %RANDOM
Rwork0.17539 ---
obs0.17588 90675 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.036 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2--2.77 Å20 Å2
3----4.83 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8362 0 99 742 9203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228725
X-RAY DIFFRACTIONr_bond_other_d0.0020.025917
X-RAY DIFFRACTIONr_angle_refined_deg1.251.96811926
X-RAY DIFFRACTIONr_angle_other_deg0.923.00214264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26351068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52922.897397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98151259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1631572
X-RAY DIFFRACTIONr_chiral_restr0.0750.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021859
X-RAY DIFFRACTIONr_nbd_refined0.1970.21798
X-RAY DIFFRACTIONr_nbd_other0.1960.26227
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24239
X-RAY DIFFRACTIONr_nbtor_other0.0860.24362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2512
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6671.55684
X-RAY DIFFRACTIONr_mcbond_other0.1141.52148
X-RAY DIFFRACTIONr_mcangle_it1.00428634
X-RAY DIFFRACTIONr_scbond_it1.47733743
X-RAY DIFFRACTIONr_scangle_it2.3614.53292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 102 -
Rwork0.224 4787 -
obs--72.99 %
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)
10.5621-0.11390.10450.4962-0.27071.4809-0.05810.0133-0.02630.0115-0.007-0.00540.1098-0.03590.0651-0.0659-0.0085-0.0019-0.10290.0314-0.028227.581112.205416.9404
20.448-0.00310.17420.64210.36961.78550.07780.0167-0.01850.0336-0.11910.08020.1181-0.01990.0413-0.086-0.0093-0.0127-0.0761-0.0656-0.05877.66184.5363-40.3292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 5431 - 543
2X-RAY DIFFRACTION2BB4 - 5434 - 543

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