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

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Basic information

Entry
Database: PDB / ID: 6cqt
TitleCrystal Structure of Recombinant Human Acetylcholinesterase Inhibited by (-) Stereoisomer of VX
ComponentsAcetylcholinesterase
KeywordsHYDROLASE
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-7PE / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.273 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_struct_special_symmetry / 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.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_struct_special_symmetry.label_asym_id / _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_2 / _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)121,34710
Polymers118,8942
Non-polymers2,4528
Water20,8971160
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,34710
Polymers118,8942
Non-polymers2,4528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y,x-1,-z1
Buried area5450 Å2
ΔGint28 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.368, 104.368, 323.224
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1134-

HOH

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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, 1164 molecules

#4: 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.: 2 / Source method: obtained synthetically / Formula: C14H30O7
#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.: 1160 / 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: 4.27 Å3/Da / Density % sol: 71.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1:1:1 ratio of DMSO, glycerol, and ethylene glycol, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 94496 / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.032 / Net I/σ(I): 25.8
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.6 / Rpim(I) all: 0.15 / % possible all: 97.3

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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: 2.273→45.193 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 4740 5.02 %
Rwork0.1485 --
obs0.1501 94419 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.273→45.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8258 0 158 1160 9576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068823
X-RAY DIFFRACTIONf_angle_d0.94912071
X-RAY DIFFRACTIONf_dihedral_angle_d15.7915184
X-RAY DIFFRACTIONf_chiral_restr0.0721302
X-RAY DIFFRACTIONf_plane_restr0.0061582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2733-2.29920.23881400.18982775X-RAY DIFFRACTION95
2.2992-2.32620.21371380.18372980X-RAY DIFFRACTION99
2.3262-2.35460.23221590.17452955X-RAY DIFFRACTION100
2.3546-2.38440.20841690.16912980X-RAY DIFFRACTION100
2.3844-2.41580.17281570.16412965X-RAY DIFFRACTION100
2.4158-2.44890.1831530.15992954X-RAY DIFFRACTION100
2.4489-2.48380.22861680.16272990X-RAY DIFFRACTION100
2.4838-2.52090.19661320.16252936X-RAY DIFFRACTION100
2.5209-2.56030.21231550.16663002X-RAY DIFFRACTION100
2.5603-2.60230.18281570.16352985X-RAY DIFFRACTION100
2.6023-2.64710.24061430.16372969X-RAY DIFFRACTION100
2.6471-2.69530.21281590.1592989X-RAY DIFFRACTION100
2.6953-2.74710.19461220.15563042X-RAY DIFFRACTION100
2.7471-2.80320.20171470.15942961X-RAY DIFFRACTION100
2.8032-2.86410.19611700.15532951X-RAY DIFFRACTION100
2.8641-2.93070.1962040.15732928X-RAY DIFFRACTION100
2.9307-3.0040.18461580.1513021X-RAY DIFFRACTION100
3.004-3.08520.19511780.14742972X-RAY DIFFRACTION100
3.0852-3.1760.1711680.14342983X-RAY DIFFRACTION100
3.176-3.27840.17391450.15022997X-RAY DIFFRACTION100
3.2784-3.39560.16431750.14292980X-RAY DIFFRACTION100
3.3956-3.53150.19231550.14082977X-RAY DIFFRACTION100
3.5315-3.69210.17571740.13773026X-RAY DIFFRACTION100
3.6921-3.88670.14521530.12542998X-RAY DIFFRACTION99
3.8867-4.13010.1661560.11893013X-RAY DIFFRACTION99
4.1301-4.44870.13971540.11782998X-RAY DIFFRACTION99
4.4487-4.89590.13731390.11393069X-RAY DIFFRACTION99
4.8959-5.60320.15881480.14843058X-RAY DIFFRACTION99
5.6032-7.05510.18761810.17283069X-RAY DIFFRACTION99
7.0551-45.20160.20761830.18683156X-RAY DIFFRACTION97
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)
11.62360.45990.62431.34860.1822.2144-0.0314-0.152-0.00790.08870.04310.0447-0.127-0.157-0.01630.15390.0456-0.02080.27150.02070.164453.259130.955335.0173
21.49290.51540.93891.32050.6191.73480.03090.1603-0.1029-0.09640.0258-0.0863-0.03970.1915-0.05610.16670.001-0.00230.28330.00750.150558.19426.562612.6115
33.6391-0.2433-0.24542.13740.0712.9119-0.06860.29080.2444-0.13570.0367-0.1043-0.3830.20610.02560.329-0.0396-0.03590.32830.02950.167454.889136.56726.3336
41.1494-0.1317-0.22821.02110.00331.87150.0488-0.0609-0.07380.1875-0.08820.01360.00250.11220.03650.1578-0.0754-0.0090.19990.02880.1889107.446532.240239.8009
50.7027-0.0132-0.03470.7115-0.24351.61530.06690.10640.0589-0.0289-0.0995-0.028-0.23650.08340.02530.1713-0.0313-0.00790.22730.02140.1842107.269445.580722.9737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:320)
2X-RAY DIFFRACTION2(chain A and resid 321:490)
3X-RAY DIFFRACTION3(chain A and resid 491:542)
4X-RAY DIFFRACTION4(chain B and resid 4:257)
5X-RAY DIFFRACTION5(chain B and resid 258:542)

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