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- PDB-2ha2: Crystal structure of mouse acetylcholinesterase complexed with su... -

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Basic information

Entry
Database: PDB / ID: 2ha2
TitleCrystal structure of mouse acetylcholinesterase complexed with succinylcholine
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / HYDROLASE FOLD / SERINE ESTERASE / ACETYLCHOLINESTERASE / HOMODIMER / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane / collagen binding / laminin binding / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / 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
alpha-L-fucopyranose / Chem-SCK / Chem-SCU / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 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 / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
Revision 2.2Oct 23, 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)121,80011
Polymers119,5292
Non-polymers2,2719
Water13,763764
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.935, 110.487, 227.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 , 3 types, 4 molecules

#2: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: 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 , 4 types, 769 molecules

#5: Chemical ChemComp-SCK / 2,2'-[(1,4-DIOXOBUTANE-1,4-DIYL)BIS(OXY)]BIS(N,N,N-TRIMETHYLETHANAMINIUM) / SUCCINYLDICHOLINE


Mass: 290.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30N2O4
#6: Chemical ChemComp-SCU / N,N,N-TRIMETHYL-2-[(4-OXOBUTANOYL)OXY]ETHANAMINIUM / SUCCINYLMONOCHOLINE


Mass: 188.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18NO3
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsSCK(901) AND SCU(902) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. SCK(951) AND SCU(952) ARE IN ...SCK(901) AND SCU(902) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. SCK(951) AND SCU(952) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 4.15 Å3/Da / Density % sol: 70.38 %
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: 2.05→30 Å / Num. obs: 112415 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.6
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 1.4 / % possible all: 55.1

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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: 2.05→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.462 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22158 2255 2 %RANDOM
Rwork0.19168 ---
obs0.19227 110041 89.87 %-
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: 46.049 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2--4.21 Å20 Å2
3----6.46 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8350 0 151 764 9265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228813
X-RAY DIFFRACTIONr_bond_other_d0.0020.025984
X-RAY DIFFRACTIONr_angle_refined_deg1.411.97312043
X-RAY DIFFRACTIONr_angle_other_deg1.0453.00214422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50851078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05722.775400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.555151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9081575
X-RAY DIFFRACTIONr_chiral_restr0.1120.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021882
X-RAY DIFFRACTIONr_nbd_refined0.2050.21929
X-RAY DIFFRACTIONr_nbd_other0.2010.26471
X-RAY DIFFRACTIONr_nbtor_refined0.1810.24352
X-RAY DIFFRACTIONr_nbtor_other0.090.24468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2603
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0210.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7341.55717
X-RAY DIFFRACTIONr_mcbond_other0.1431.52154
X-RAY DIFFRACTIONr_mcangle_it1.08228656
X-RAY DIFFRACTIONr_scbond_it1.64633816
X-RAY DIFFRACTIONr_scangle_it2.5314.53383
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 105 -
Rwork0.315 4568 -
obs--54.47 %
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)
11.2867-0.06450.08250.7276-0.3062.5147-0.03110.0043-0.05880.030.01090.01980.1415-0.12410.0202-0.14920.00680.0054-0.2730.034-0.047427.522511.789716.7255
20.7986-0.12050.11320.93870.38882.77170.13750.0095-0.04780.0194-0.09920.05290.1737-0.0139-0.0383-0.105-0.0204-0.028-0.1106-0.0737-0.05937.96114.6044-40.8283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 5421 - 542
2X-RAY DIFFRACTION2BB4 - 5434 - 543

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