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

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Basic information

Entry
Database: PDB / ID: 6cqz
TitleCrystal Structure of Recombinant Human Acetylcholinesterase Inhibited by 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
O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.216 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.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 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 9, 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)120,5057
Polymers118,8942
Non-polymers1,6105
Water20,1051116
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5057
Polymers118,8942
Non-polymers1,6105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_647y+1,x-1,-z+21
Buried area4420 Å2
ΔGint23 kcal/mol
Surface area38090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.601, 104.601, 323.752
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-851-

HOH

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 59447.105 Da / Num. of mol.: 2 / Fragment: UNP residues 33-574
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.: 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.: 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
#4: Chemical ChemComp-VX / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP


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


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 4.3 Å3/Da / Density % sol: 71.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12 to 18% PEG 3350, 0.2M 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.216→50 Å / Num. obs: 94149 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.048 / Net I/σ(I): 16.6
Reflection shellResolution: 2.216→2.26 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 5.2 / Rpim(I) all: 0.165 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.216→40.686 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.8
RfactorNum. reflection% reflection
Rfree0.1935 4688 4.98 %
Rwork0.1658 --
obs0.1672 94144 91.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.216→40.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8234 0 102 1119 9455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038645
X-RAY DIFFRACTIONf_angle_d0.72211827
X-RAY DIFFRACTIONf_dihedral_angle_d2.5876898
X-RAY DIFFRACTIONf_chiral_restr0.0471276
X-RAY DIFFRACTIONf_plane_restr0.0051552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2158-2.24090.2493630.21971529X-RAY DIFFRACTION47
2.2409-2.26730.26551020.20771670X-RAY DIFFRACTION52
2.2673-2.29490.2441930.2121908X-RAY DIFFRACTION60
2.2949-2.3240.2209860.20982120X-RAY DIFFRACTION64
2.324-2.35460.21181540.22062233X-RAY DIFFRACTION72
2.3546-2.38680.25651320.22222528X-RAY DIFFRACTION78
2.3868-2.42090.26471380.22212778X-RAY DIFFRACTION86
2.4209-2.4570.24861600.21182932X-RAY DIFFRACTION92
2.457-2.49540.26861520.20873145X-RAY DIFFRACTION96
2.4954-2.53630.25321500.19993141X-RAY DIFFRACTION97
2.5363-2.58010.24631400.19633207X-RAY DIFFRACTION99
2.5801-2.6270.21551800.19653216X-RAY DIFFRACTION99
2.627-2.67750.2111440.1983245X-RAY DIFFRACTION99
2.6775-2.73210.21321870.18793185X-RAY DIFFRACTION100
2.7321-2.79150.22391800.18763223X-RAY DIFFRACTION100
2.7915-2.85650.21062030.18073210X-RAY DIFFRACTION100
2.8565-2.92790.2271660.1763258X-RAY DIFFRACTION100
2.9279-3.0070.18611570.16553245X-RAY DIFFRACTION100
3.007-3.09550.18061860.16923243X-RAY DIFFRACTION100
3.0955-3.19530.20681600.1653265X-RAY DIFFRACTION100
3.1953-3.30950.18271650.16573259X-RAY DIFFRACTION100
3.3095-3.44190.18681660.15463264X-RAY DIFFRACTION100
3.4419-3.59850.1681690.1523296X-RAY DIFFRACTION100
3.5985-3.78810.17761930.14153255X-RAY DIFFRACTION100
3.7881-4.02520.16061830.12893291X-RAY DIFFRACTION100
4.0252-4.33570.14721850.12823277X-RAY DIFFRACTION100
4.3357-4.77140.14681580.12263334X-RAY DIFFRACTION100
4.7714-5.46040.15281860.14393314X-RAY DIFFRACTION100
5.4604-6.87420.2031710.17733382X-RAY DIFFRACTION100
6.8742-40.69290.22341790.18063503X-RAY DIFFRACTION98
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)
11.72440.5494-0.43691.1287-0.01642.005-0.067-0.0960.0590.04720.065-0.02050.15290.1598-0.00060.12240.04970.02470.2113-0.01180.147150.9351-31.0455358.8917
21.22920.5201-0.96480.7622-0.70461.99060.00490.14310.0819-0.12150.03520.07180.0437-0.2065-0.03380.2217-0.02520.020.2827-0.01470.201547.1376-28.8779335.0012
31.2053-0.43340.08896.8063-0.44570.0325-0.0947-0.38180.1040.61430.0845-0.0001-0.09170.19880.09810.3947-0.0797-0.02340.2578-0.03940.1873107.1485-35.3731381.6957
41.0309-0.37440.14511.08630.06131.46340.0526-0.00670.07950.1422-0.0928-0.0076-0.0175-0.14010.01070.1195-0.07940.00920.1742-0.01970.1804100.6144-31.9624361.5071
52.1581-0.6337-0.5761.43020.231.54150.12540.37630.0132-0.2939-0.18970.1975-0.1288-0.33880.05990.18450.0176-0.02590.3561-0.01940.258690.5429-26.9687348.2259
60.65450.02270.47460.65320.42372.44220.05470.0813-0.09340.0029-0.1122-0.00390.3313-0.13370.03440.1787-0.03570.01830.2028-0.03690.1911104.2559-50.3179346.405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:317)
2X-RAY DIFFRACTION2(chain A and resid 318:542)
3X-RAY DIFFRACTION3(chain B and resid 4:31)
4X-RAY DIFFRACTION4(chain B and resid 32:257)
5X-RAY DIFFRACTION5(chain B and resid 258:315)
6X-RAY DIFFRACTION6(chain B and resid 316:542)

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