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- PDB-4bdt: Human acetylcholinesterase in complex with huprine W and fasciculin 2 -

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Basic information

Entry
Database: PDB / ID: 4bdt
TitleHuman acetylcholinesterase in complex with huprine W and fasciculin 2
Components
  • ACETYLCHOLINESTERASE
  • FASCICULIN-2
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / BUTYRYLCHOLINESTERASE / NERVE TRANSMISSION / INHIBITION / ALPHA-BETA HYDROLASE
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / choline metabolic process / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / toxin activity / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane
Similarity search - Function
Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Snake toxin-like superfamily / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. ...Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Snake toxin-like superfamily / 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 / Ribbon / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HUPRINE W / Fasciculin-2 / Acetylcholinesterase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
DENDROASPIS ANGUSTICEPS (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.104 Å
AuthorsNachon, F. / Carletti, E. / Ronco, C. / Trovaslet, M. / Nicolet, Y. / Jean, L. / Renard, P.-Y.
CitationJournal: Biochem. J. / Year: 2013
Title: Crystal structures of human cholinesterases in complex with huprine W and tacrine: elements of specificity for anti-Alzheimer's drugs targeting acetyl- and butyryl-cholinesterase.
Authors: Nachon, F. / Carletti, E. / Ronco, C. / Trovaslet, M. / Nicolet, Y. / Jean, L. / Renard, P.Y.
History
DepositionOct 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Feb 28, 2018Group: Advisory / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_seq_id / _struct_conn.ptnr1_label_atom_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: FASCICULIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,74615
Polymers71,4112
Non-polymers1,33613
Water2,144119
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,95528
Polymers129,2832
Non-polymers2,67226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
Buried area6750 Å2
ΔGint-155.7 kcal/mol
Surface area42860 Å2
MethodPISA
2
A: ACETYLCHOLINESTERASE
B: FASCICULIN-2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)436,47990
Polymers428,46312
Non-polymers8,01678
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
Buried area43490 Å2
ΔGint-553.3 kcal/mol
Surface area129720 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-71.5 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.600, 151.600, 246.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2086-

HOH

DetailsCHAINA FORMS A BIOLOGICAL DIMER WITH A SYMMETRIC MOLECULE BY INTERACTION OF 4 HELICES. THE DODECAMETRIC ASSEMBLY SHOWN IN THE ASSEMBLY INFORMATION RESULTS FROM THE ASSOCIATION OF 3 BIOLOGICAL DIMERS.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 64641.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGS / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P22303, acetylcholinesterase
#2: Protein FASCICULIN-2 / FAS-2 / FAS2 / ACETYLCHOLINESTERASE TOXIN F-VII / FASCICULIN-II / FAS-II / TOXIN TA1


Mass: 6768.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) DENDROASPIS ANGUSTICEPS (eastern green mamba)
References: UniProt: P0C1Z0

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 131 molecules

#4: Chemical ChemComp-HUW / HUPRINE W


Mass: 314.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19ClN2O
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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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: 4.9 Å3/Da / Density % sol: 75 % / Description: NONE
Crystal growpH: 7.4 / Details: 0.1 M HEPES BUFFER PH 7.4, 1.3 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→58 Å / Num. obs: 19677 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 66.43 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X8B

2x8b


Resolution: 3.104→57.934 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 982 5 %
Rwork0.159 --
obs0.1621 19627 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.2 Å2
Refinement stepCycle: LAST / Resolution: 3.104→57.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4863 0 75 119 5057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085088
X-RAY DIFFRACTIONf_angle_d1.2916945
X-RAY DIFFRACTIONf_dihedral_angle_d18.3191845
X-RAY DIFFRACTIONf_chiral_restr0.082738
X-RAY DIFFRACTIONf_plane_restr0.007910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1041-3.26770.3821370.26272599X-RAY DIFFRACTION97
3.2677-3.47240.32331390.22562625X-RAY DIFFRACTION99
3.4724-3.74050.25581400.18012666X-RAY DIFFRACTION99
3.7405-4.11680.21021410.13852667X-RAY DIFFRACTION99
4.1168-4.71230.19321400.11832663X-RAY DIFFRACTION99
4.7123-5.9360.16581410.13922694X-RAY DIFFRACTION99
5.936-57.9440.1921440.15682731X-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)
11.4688-0.18640.09541.0520.08141.67330.0257-0.03420.07480.0915-0.0296-0.0205-0.1714-0.0290.03160.28870.0340.01660.08940.05420.20810.4631-40.5065-58.4343
21.11860.0830.75360.01570.04230.53670.093-0.61020.2410.434-0.0970.3343-0.9828-0.39260.00220.70410.10270.06650.37120.0080.4119-19.4319-36.7207-38.2366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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