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- PDB-8p22: X-ray structure of acetylcholine-binding protein (AChBP) in compl... -

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Basic information

Entry
Database: PDB / ID: 8p22
TitleX-ray structure of acetylcholine-binding protein (AChBP) in complex with IOTA376.
ComponentsAcetylcholine-binding protein
KeywordsCHOLINE-BINDING PROTEIN / Fragment based drug design / Acetylcholine-binding protein / choline-binding proteins
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / synapse / membrane
Similarity search - Function
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 / Ig-like domain profile. / Immunoglobulin-like domain
Similarity search - Domain/homology
: / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCederfelt, D. / Boronat, P. / Dobritzsch, D. / Hennig, S. / Fitzgerald, E.A. / de Esch, I.J.P. / Danielson, U.H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675899European Union
CitationJournal: To Be Published
Title: Elucidating the regulation of ligand gated ion channels via biophysical studies of ligand-induced conformational dynamics of acetylcholine binding proteins
Authors: Fitzgerald, E.A. / Cederfelt, D. / Boronat, P. / Aarmo Lund, B. / Dobritzsch, D. / de Esch, I.J.P. / Danielson, U.H.
History
DepositionMay 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 1, 2025Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: pdbx_contact_author / pdbx_entity_instance_feature ...pdbx_contact_author / pdbx_entity_instance_feature / pdbx_struct_assembly / refine / refine_ls_shell / reflns / reflns_shell
Item: _pdbx_struct_assembly.details / _refine.B_iso_mean ..._pdbx_struct_assembly.details / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,21023
Polymers234,54010
Non-polymers2,66913
Water14,862825
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33400 Å2
ΔGint-166 kcal/mol
Surface area79440 Å2
Unit cell
Length a, b, c (Å)143.960, 120.600, 133.160
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 23454.029 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P58154
#2: Chemical
ChemComp-WNO / 2-[(2~{R})-1-ethylimidazolidin-2-yl]-6-pyridin-2-yl-pyridine


Mass: 254.330 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H18N4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350 3% Ammonium sulphate 1.8M HEPES buffer 0.1M, pH 7.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.53→49.51 Å / Num. obs: 101963 / % possible obs: 88.32 % / Redundancy: 2 % / CC1/2: 0.907 / Rmerge(I) obs: 0.1379 / Rrim(I) all: 0.1852 / Net I/σ(I): 7.41
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.6544 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 10549 / CC1/2: 0.588 / Rrim(I) all: 0.8643 / % possible all: 91.57

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.51 Å / Cor.coef. Fo:Fc: 0.945 / SU B: 11.666 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3038 --RANDOM
Rwork0.2381 ---
obs-101774 88.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20.09 Å2
2---0.09 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16185 0 15 825 17025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01216594
X-RAY DIFFRACTIONr_bond_other_d0.0020.01615227
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.80322635
X-RAY DIFFRACTIONr_angle_other_deg0.5741.76135057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.70551978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.7576.078167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.877102697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.22563
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023943
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2254.6427972
X-RAY DIFFRACTIONr_mcbond_other4.2254.6427972
X-RAY DIFFRACTIONr_mcangle_it6.4388.3229930
X-RAY DIFFRACTIONr_mcangle_other6.4388.3229931
X-RAY DIFFRACTIONr_scbond_it4.5595.0968622
X-RAY DIFFRACTIONr_scbond_other4.5275.0948611
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0599.1512688
X-RAY DIFFRACTIONr_long_range_B_refined10.64145.5518776
X-RAY DIFFRACTIONr_long_range_B_other10.62145.3518675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.279 Å
RfactorNum. reflection% reflection
Rfree0.4053 --
Rwork0.4053 10549 -
obs--91.57 %

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