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- PDB-5hf9: Crystal structure of human acetylcholinesterase in complex with p... -

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Basic information

Entry
Database: PDB / ID: 5hf9
TitleCrystal structure of human acetylcholinesterase in complex with paraoxon and HI6
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / positive regulation of protein secretion / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / nervous system development / amyloid-beta binding / cell adhesion / hydrolase activity / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / 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 ...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
DIETHYL PHOSPHONATE / Chem-HI6 / NITRATE ION / 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: 2.2 Å
AuthorsFranklin, M.F. / Rudolph, M.J. / Ginter, C. / Cassidy, M.S. / Cheung, J.
CitationJournal: Proteins / Year: 2016
Title: Structures of paraoxon-inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer interface.
Authors: Franklin, M.C. / Rudolph, M.J. / Ginter, C. / Cassidy, M.S. / Cheung, J.
History
DepositionJan 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)121,79015
Polymers118,8942
Non-polymers2,89613
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint58 kcal/mol
Surface area37990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.931, 105.931, 324.415
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59447.105 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 33 to 574 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase

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Sugars , 2 types, 3 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 6 types, 600 molecules

#3: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H11O3P
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-HI6 / 4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM / 1-(2-HYDROXY-IMINOMETHYLPYRIDINIUM)-1-(4-CARBOXYAMINO)-PYRIDINIUM DIMETHYLETHER


Mass: 288.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N4O3
#7: 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
#8: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.44 Å3/Da / Density % sol: 72.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15 - 18% PEG3350, 0.2M potassium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 108212 / % possible obs: 99.6 % / Redundancy: 7.8 % / Biso Wilson estimate: 34.06 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.052 / Rrim(I) all: 0.135 / Χ2: 1.05 / Net I/av σ(I): 16.488 / Net I/σ(I): 5.2 / Num. measured all: 844881
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRmerge(I) obsRpim(I) allRrim(I) all
2.2-2.246.453440.6730.557100
2.24-2.285.150660.9641.14594.60.6750.3650.776
2.28-2.328.453640.7720.5711000.418
2.32-2.378.453510.8370.5631000.9470.341
2.37-2.428.354040.8610.581000.7930.2870.845
2.42-2.488.353480.9050.5821000.6350.230.677
2.48-2.548.253610.9250.6211000.5530.20.589
2.54-2.618.253650.950.6211000.4270.1550.456
2.61-2.697.753710.9420.85699.90.4290.1650.461
2.69-2.778.154250.9720.7251000.3410.1240.364
2.77-2.878.254060.9810.7091000.2460.0890.262
2.87-2.998.353740.9860.7841000.2020.0730.215
2.99-3.128.254370.9910.8961000.1650.060.176
3.12-3.298.153920.9921.0291000.1420.0520.152
3.29-3.497.654130.9911.28899.90.1280.050.138
3.49-3.767.254590.9931.47299.60.1040.0420.113
3.76-4.146.953880.9931.7398.70.0870.0370.095
4.14-4.747.655140.9951.98399.90.0760.030.082
4.74-5.978.455960.9961.9971000.0740.0280.08
5.97-508.558340.9972.26599.70.0640.0240.069

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.2→45.418 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 5346 5.01 %random
Rwork0.2009 101279 --
obs0.2029 106625 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.01 Å2 / Biso mean: 48.1514 Å2 / Biso min: 26.44 Å2
Refinement stepCycle: final / Resolution: 2.2→45.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8268 0 193 590 9051
Biso mean--70.17 51.98 -
Num. residues----1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018816
X-RAY DIFFRACTIONf_angle_d1.21412040
X-RAY DIFFRACTIONf_chiral_restr0.051286
X-RAY DIFFRACTIONf_plane_restr0.0071580
X-RAY DIFFRACTIONf_dihedral_angle_d14.7933178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1967-2.22170.42561810.383274345597
2.2217-2.24780.47021500.44722956310686
2.2478-2.27520.52131290.49172354248370
2.2752-2.3040.3461890.331833993588100
2.304-2.33430.3791660.320133573523100
2.3343-2.36630.3671810.298633663547100
2.3663-2.40010.32061880.281833933581100
2.4001-2.43590.27071790.264534143593100
2.4359-2.4740.31391740.262233883562100
2.474-2.51450.27252060.244233823588100
2.5145-2.55790.28811760.239833643540100
2.5579-2.60440.32961630.238934323595100
2.6044-2.65450.29962060.25534243630100
2.6545-2.70870.39841830.34133342352598
2.7087-2.76760.25191680.210134223590100
2.7676-2.83190.24751920.192733743566100
2.8319-2.90270.24121740.192334203594100
2.9027-2.98120.25761640.197234593623100
2.9812-3.06890.24531840.187734183602100
3.0689-3.16790.25041780.188134203598100
3.1679-3.28110.24941700.196534553625100
3.2811-3.41250.22631860.19934663652100
3.4125-3.56770.25381910.233363355499
3.5677-3.75570.24641680.21323454362299
3.7557-3.99090.23671800.19143382356298
3.9909-4.29880.2111710.156234823653100
4.2988-4.7310.15211900.130634893679100
4.731-5.41470.16211700.138835433713100
5.4147-6.81820.19822090.163635413750100
6.8182-45.42740.20171800.178237463926100

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