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- PDB-6ntl: Crystal Structure of Recombinant Human Acetylcholinesterase Inhib... -

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Basic information

Entry
Database: PDB / ID: 6ntl
TitleCrystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-234
ComponentsAcetylcholinesterase
Keywordshydrolase/hydrolase inhibitor / hydrolase / inhibitor / hydrolase-hydrolase inhibitor complex
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 ...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-7PE / Chem-L1M / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBester, S.M. / Guelta, M.A. / Height, J.J. / Pegan, S.D.
CitationJournal: To Be Published
Title: Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents
Authors: Height, J.J. / Bester, S.M. / Guelta, M.A. / Bae, S.Y. / Cheung, J. / Pegan, S.D.
History
DepositionJan 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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 11, 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 2.2Nov 13, 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)121,3298
Polymers118,8942
Non-polymers2,4346
Water18,7181039
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3298
Polymers118,8942
Non-polymers2,4346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area4630 Å2
ΔGint19 kcal/mol
Surface area38380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.966, 104.966, 323.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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
#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.: 3
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: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H30O7
#4: Chemical ChemComp-L1M / ethyl (R)-N-[(1E)-1-(diethylamino)ethylidene]phosphonamidate


Mass: 206.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19N2O2P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1039 / Source method: isolated from a natural source / Formula: H2O
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: 71.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15-21% polyethylene glycol 3350 (PEG) and 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 99121 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.045 / Net I/σ(I): 16.8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4885 / CC1/2: 0.846 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.25→46.41 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 4453 4.96 %
Rwork0.1686 --
obs0.1698 89717 90.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8252 0 161 1039 9452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048736
X-RAY DIFFRACTIONf_angle_d0.87811948
X-RAY DIFFRACTIONf_dihedral_angle_d4.6736950
X-RAY DIFFRACTIONf_chiral_restr0.0471290
X-RAY DIFFRACTIONf_plane_restr0.0051563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27510.225670.22251394X-RAY DIFFRACTION45
2.2751-2.30190.2703660.22791563X-RAY DIFFRACTION50
2.3019-2.330.25311010.22131682X-RAY DIFFRACTION54
2.33-2.35950.2482720.22731888X-RAY DIFFRACTION61
2.3595-2.39050.26621300.22582019X-RAY DIFFRACTION65
2.3905-2.42330.22971170.2252322X-RAY DIFFRACTION75
2.4233-2.45790.24341420.20952627X-RAY DIFFRACTION84
2.4579-2.49460.28341510.22212839X-RAY DIFFRACTION91
2.4946-2.53350.23021250.21712833X-RAY DIFFRACTION92
2.5335-2.57510.24931400.20262976X-RAY DIFFRACTION95
2.5751-2.61950.25631650.19923137X-RAY DIFFRACTION100
2.6195-2.66710.21421490.19283077X-RAY DIFFRACTION100
2.6671-2.71840.21461430.18533141X-RAY DIFFRACTION100
2.7184-2.77390.21441850.18413111X-RAY DIFFRACTION100
2.7739-2.83420.19911840.18323108X-RAY DIFFRACTION100
2.8342-2.90010.19541850.18713078X-RAY DIFFRACTION100
2.9001-2.97260.20611700.17633092X-RAY DIFFRACTION100
2.9726-3.0530.21621690.16833125X-RAY DIFFRACTION100
3.053-3.14280.16511560.16973135X-RAY DIFFRACTION99
3.1428-3.24420.1951580.16453143X-RAY DIFFRACTION100
3.2442-3.36010.15021480.15943167X-RAY DIFFRACTION100
3.3601-3.49460.18461690.16433147X-RAY DIFFRACTION100
3.4946-3.65360.18121640.15373139X-RAY DIFFRACTION100
3.6536-3.84610.18571640.14243148X-RAY DIFFRACTION100
3.8461-4.0870.16451910.13443122X-RAY DIFFRACTION100
4.087-4.40230.16151870.13153178X-RAY DIFFRACTION100
4.4023-4.84490.14431520.12613196X-RAY DIFFRACTION100
4.8449-5.5450.17571640.14913240X-RAY DIFFRACTION100
5.545-6.98230.19121650.18233257X-RAY DIFFRACTION100
6.9823-46.41960.21181740.18883380X-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)
11.73280.3874-0.43541.082-0.05152.2215-0.0434-0.1510.04140.06970.0383-0.04360.20710.18920.00290.16510.05380.03170.2284-0.00220.1679-1.287159.3544358.7623
21.31890.3843-1.04490.9336-0.59272.1876-0.02520.14690.0593-0.10760.0390.05090.1051-0.2044-0.01370.2039-0.01780.01640.2336-0.00770.1731-5.532662.0762334.9405
31.2867-0.21380.26271.5177-0.15871.3232-0.0187-0.19070.04060.3255-0.06290.05740.005-0.24180.08360.2308-0.08080.04170.2245-0.03630.180646.697757.3295371.4611
41.5504-0.49150.02121.25970.11241.65940.10890.14640.108-0.008-0.10270.0383-0.1009-0.1634-0.00450.1213-0.05350.01640.1897-0.01850.19347.596760.029355.3899
51.00810.26810.42490.87850.52652.44550.03060.1015-0.1169-0.0158-0.08090.0060.325-0.11260.03470.1867-0.0270.02740.2017-0.03930.196352.432540.4558346.4905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:321)
2X-RAY DIFFRACTION2(chain A and resid 322:542)
3X-RAY DIFFRACTION3(chain B and resid 4:109)
4X-RAY DIFFRACTION4(chain B and resid 110:312)
5X-RAY DIFFRACTION5(chain B and resid 313:542)

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