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- PDB-3c79: Crystal structure of Aplysia californica AChBP in complex with th... -

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Basic information

Entry
Database: PDB / ID: 3c79
TitleCrystal structure of Aplysia californica AChBP in complex with the neonicotinoid imidacloprid
ComponentsSoluble acetylcholine receptor
KeywordsCHOLINE-BINDING PROTEIN / protein-neonicotinoid complex / Receptor
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / identical protein binding / membrane / metal ion binding
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-IM4 / ISOPROPYL ALCOHOL / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsTalley, T.T. / Harel, M. / Hibbs, R.E. / Tomizawa, M. / Casida, J.E. / Taylor, P.W.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Atomic interactions of neonicotinoid agonists with AChBP: molecular recognition of the distinctive electronegative pharmacophore.
Authors: Talley, T.T. / Harel, M. / Hibbs, R.E. / Radic, Z. / Tomizawa, M. / Casida, J.E. / Taylor, P.
History
DepositionFeb 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,46712
Polymers129,2645
Non-polymers1,2037
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.390, 116.286, 132.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 25852.744 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): kidney HEK-293 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-IM4 / (2E)-1-[(6-chloropyridin-3-yl)methyl]-N-nitroimidazolidin-2-imine / imidacloprid


Mass: 255.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H10ClN5O2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% isopropanol, 0.2M magnesium chloride, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→47.72 Å / Num. all: 46414 / Num. obs: 44102 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.8
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4 / Num. unique all: 7210 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2byn

2byn


Resolution: 2.48→47.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 17.172 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.457 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25047 2355 5.1 %RANDOM
Rwork0.18763 ---
obs0.19084 44045 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---1.09 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.48→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8414 0 80 124 8618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0228740
X-RAY DIFFRACTIONr_angle_refined_deg2.2731.9611913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57951053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33624.313415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.631151418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2761553
X-RAY DIFFRACTIONr_chiral_restr0.1520.21315
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026727
X-RAY DIFFRACTIONr_nbd_refined0.2330.23655
X-RAY DIFFRACTIONr_nbtor_refined0.3290.26011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2400
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5770.24
X-RAY DIFFRACTIONr_mcbond_it1.531.55455
X-RAY DIFFRACTIONr_mcangle_it2.39528663
X-RAY DIFFRACTIONr_scbond_it3.94733877
X-RAY DIFFRACTIONr_scangle_it5.634.53249
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 173 -
Rwork0.252 3194 -
obs-3194 97.23 %
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)
10.5434-0.0713-0.28561.13850.01791.24-0.0214-0.0203-0.0147-0.05840.0245-0.2737-0.03480.091-0.0031-0.0758-0.00770.0019-0.04090.0320.018360.853-3.087-0.513
21.04240.2409-0.16311.0499-0.24320.79030.0275-0.00220.1645-0.03240.0046-0.033-0.0342-0.0103-0.0321-0.01730.0021-0.0086-0.0661-0.002-0.023647.32919.8581.785
30.78810.10470.13970.88970.07480.5782-0.00310.03570.1081-0.04790.01470.2366-0.00490.0184-0.0116-0.03720.0142-0.0163-0.0628-0.00430.015121.53614.497-0.2
40.7672-0.2373-0.00120.70960.3661.8435-0.0207-0.0188-0.0961-0.0522-0.04070.25570.0139-0.04660.0614-0.0585-0.0368-0.008-0.07060.00730.01418.553-11.946-3.316
51.19150.247-0.06170.8315-0.10171.1913-0.01470.055-0.2257-0.05240.0463-0.08410.05690.0208-0.0316-0.03490.01860.02-0.0980.02090.026143.14-23.006-3.501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 2086 - 216
2X-RAY DIFFRACTION2BB-3 - 2085 - 216
3X-RAY DIFFRACTION3CC-1 - 2087 - 216
4X-RAY DIFFRACTION4DD-3 - 2085 - 216
5X-RAY DIFFRACTION5EE-3 - 2085 - 216

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