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- PDB-6cqy: Crystal Structure of Recombinant Human Acetylcholinesterase in Co... -

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Basic information

Entry
Database: PDB / ID: 6cqy
TitleCrystal Structure of Recombinant Human Acetylcholinesterase in Complex with EMPA and HI-6
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Hydrolase Cholinesterase
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 / cell adhesion / hydrolase activity / 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 ...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
Chem-HI6 / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.449 Å
AuthorsBester, S.M. / Guelta, M.A. / Pegan, S.D. / Height, J.J.
CitationJournal: Chem. Res. Toxicol. / Year: 2018
Title: Structural Insights of Stereospecific Inhibition of Human Acetylcholinesterase by VX and Subsequent Reactivation by HI-6.
Authors: Bester, S.M. / Guelta, M.A. / Cheung, J. / Winemiller, M.D. / Bae, S.Y. / Myslinski, J. / Pegan, S.D. / Height, J.J.
History
DepositionMar 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
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 / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _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.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 4, 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)121,30210
Polymers118,8942
Non-polymers2,4088
Water9,188510
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,30210
Polymers118,8942
Non-polymers2,4088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655y+1,x,-z1
Buried area6160 Å2
ΔGint34 kcal/mol
Surface area37580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.152, 105.152, 324.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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
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, 4 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
#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, 514 molecules

#4: 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
#5: Chemical ChemComp-VX / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP


Mass: 124.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O3P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 4.35 Å3/Da / Density % sol: 71.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15 to 21% PEG 3350, 0.17 - 0.21M potassium nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.449→50 Å / Num. obs: 77545 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.031 / Net I/σ(I): 20
Reflection shellResolution: 2.449→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7586 / Rpim(I) all: 0.275 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.449→43.837 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.2
RfactorNum. reflection% reflection
Rfree0.2001 3880 5.01 %
Rwork0.1713 --
obs0.1727 77487 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.449→43.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8247 0 160 510 8917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048801
X-RAY DIFFRACTIONf_angle_d0.80612051
X-RAY DIFFRACTIONf_dihedral_angle_d15.2095153
X-RAY DIFFRACTIONf_chiral_restr0.0721300
X-RAY DIFFRACTIONf_plane_restr0.0061581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4487-2.47860.29561370.26272507X-RAY DIFFRACTION98
2.4786-2.510.29141350.242614X-RAY DIFFRACTION100
2.51-2.5430.24721340.22282594X-RAY DIFFRACTION100
2.543-2.57780.25711460.22162593X-RAY DIFFRACTION100
2.5778-2.61460.2641540.20692569X-RAY DIFFRACTION100
2.6146-2.65370.24241470.21382570X-RAY DIFFRACTION100
2.6537-2.69510.25091550.20392612X-RAY DIFFRACTION100
2.6951-2.73930.28331070.21022610X-RAY DIFFRACTION100
2.7393-2.78650.26851370.2042589X-RAY DIFFRACTION100
2.7865-2.83720.2481480.20562619X-RAY DIFFRACTION100
2.8372-2.89180.2441300.20672582X-RAY DIFFRACTION100
2.8918-2.95080.21131390.20032604X-RAY DIFFRACTION100
2.9508-3.01490.2481110.19182653X-RAY DIFFRACTION100
3.0149-3.0850.25451600.18992596X-RAY DIFFRACTION100
3.085-3.16220.21821300.18542599X-RAY DIFFRACTION100
3.1622-3.24760.22921210.18732626X-RAY DIFFRACTION100
3.2476-3.34320.21351670.1832585X-RAY DIFFRACTION100
3.3432-3.4510.19631160.18822652X-RAY DIFFRACTION100
3.451-3.57430.21331230.18062648X-RAY DIFFRACTION100
3.5743-3.71740.17171480.17172649X-RAY DIFFRACTION100
3.7174-3.88640.18851320.14692626X-RAY DIFFRACTION100
3.8864-4.09120.16171430.13892624X-RAY DIFFRACTION100
4.0912-4.34730.1751510.14182662X-RAY DIFFRACTION100
4.3473-4.68260.13891420.1262636X-RAY DIFFRACTION100
4.6826-5.15320.15091520.13482685X-RAY DIFFRACTION100
5.1532-5.89730.19291170.16052714X-RAY DIFFRACTION100
5.8973-7.42420.22241490.17912733X-RAY DIFFRACTION100
7.4242-43.84390.19041490.17382856X-RAY DIFFRACTION99
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)
12.3268-0.63932.32589.4913-1.07637.0912-0.0144-0.8153-0.03260.6944-0.16260.94750.6987-0.76240.18120.8465-0.1070.10240.6717-0.00280.531134.9984-44.109949.825
22.24130.2225-0.94291.44-0.42223.0787-0.077-0.3281-0.03490.12720.0155-0.00180.43130.13740.05570.41070.04850.03880.398-0.02430.30849.1365-32.899335.545
32.274-0.5598-0.10472.78260.52424.1385-0.1451-0.43870.24980.09850.056-0.1756-0.37810.73760.07190.367-0.03390.0130.6389-0.05770.441965.2127-21.537232.8128
41.80670.2657-1.08281.3777-0.67182.8624-0.03710.18810.0519-0.15040.0550.07590.2247-0.259-0.02580.3666-0.01650.00540.3877-0.01590.303447.1704-27.434813.1121
53.3593-0.82270.3372.0065-0.06972.7842-0.02640.4679-0.3342-0.1038-0.06550.06720.5802-0.11980.11310.6314-0.03290.0670.4428-0.01270.328749.9106-36.83346.4169
61.1578-0.456601.42060.1512.52510.0597-0.10370.04440.1942-0.04560.0458-0.0798-0.2273-0.00980.3139-0.1169-0.00220.3649-0.03160.3562-2.9285-32.937840.0538
70.7250.0343-0.00990.84420.25372.26450.0540.1337-0.0778-0.0344-0.11920.05520.2381-0.20060.05860.3591-0.08110.01070.4352-0.02310.3832-2.7048-46.120323.0265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:13)
2X-RAY DIFFRACTION2(chain A and resid 14:256)
3X-RAY DIFFRACTION3(chain A and resid 257:313)
4X-RAY DIFFRACTION4(chain A and resid 314:490)
5X-RAY DIFFRACTION5(chain A and resid 491:542)
6X-RAY DIFFRACTION6(chain B and resid 4:257)
7X-RAY DIFFRACTION7(chain B and resid 258:542)

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