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- PDB-3c84: Crystal structure of a complex of AChBP from aplysia californica ... -

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Basic information

Entry
Database: PDB / ID: 3c84
TitleCrystal structure of a complex of AChBP from aplysia californica and the neonicotinoid thiacloprid
ComponentsSoluble acetylcholine receptor
KeywordsCHOLINE-BINDING PROTEIN / acetylcholine binding protein / neonicotinoid / Receptor
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / membrane
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
ISOPROPYL ALCOHOL / Chem-TH4 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 8, 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 20, 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: 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)130,74418
Polymers129,2645
Non-polymers1,48013
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.893, 116.726, 132.002
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-TH4 / {(2Z)-3-[(6-chloropyridin-3-yl)methyl]-1,3-thiazolidin-2-ylidene}cyanamide


Mass: 252.723 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9ClN4S
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% isopropanol, 0.2M magnesium chloride, 0.1M 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: 1.94→87.4 Å / Num. all: 97540 / Num. obs: 94127 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 21
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9613 / % possible all: 100

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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: 1.94→87.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.608 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21501 4876 5 %RANDOM
Rwork0.18602 ---
obs0.18747 92566 99.73 %-
all-97540 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---1.09 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 1.94→87.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8309 0 94 478 8881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228707
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.95911877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44251055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97424.369412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.429151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9321551
X-RAY DIFFRACTIONr_chiral_restr0.1080.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026701
X-RAY DIFFRACTIONr_nbd_refined0.20.23753
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2621
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.29
X-RAY DIFFRACTIONr_mcbond_it1.1521.55480
X-RAY DIFFRACTIONr_mcangle_it1.69428644
X-RAY DIFFRACTIONr_scbond_it2.77433822
X-RAY DIFFRACTIONr_scangle_it3.9774.53229
LS refinement shellResolution: 1.939→1.989 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 316 -
Rwork0.21 6625 -
obs--98.08 %
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)
10.17520.02810.02150.4908-0.03750.1789-0.0116-0.01870.0369-0.0310.00310.15230.0226-0.01120.0085-0.02470.0006-0.0074-0.0173-0.02840.0071-18.02712.930765.4274
20.35540.09840.12380.3581-0.01430.12240.0191-0.0135-0.071-0.0129-0.01120.03160.01570.0138-0.00790.0027-0.00180.0059-0.0241-0.0069-0.0213-4.371-20.010468.0757
30.2821-0.0217-0.00690.365-0.0360.00380.0020.0066-0.05-0.0204-0.0105-0.0990.0057-0.02280.0085-0.0020.00450.0057-0.0191-0.0059-0.012721.3455-14.464965.7132
40.2759-0.05820.05660.2521-0.00650.2449-0.0113-0.00220.0404-0.0204-0.0183-0.1407-0.016-0.02420.0296-0.0166-0.00250.0063-0.0252-0.0050.001724.052411.868262.4287
50.27430.0354-0.02740.4103-0.02260.26470.01250.01930.0903-0.01890.02280.04720.00690.0038-0.0353-0.01520.0106-0.0089-0.0191-0.0154-0.0081-0.301723.01462.7015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 2076 - 215
2X-RAY DIFFRACTION2BB-3 - 2085 - 216
3X-RAY DIFFRACTION3CC-2 - 2076 - 215
4X-RAY DIFFRACTION4DD-1 - 2087 - 216
5X-RAY DIFFRACTION5EE-2 - 2076 - 215

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