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- PDB-8qx2: Aplysia californica acetylcholine-binding protein in complex with... -

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Basic information

Entry
Database: PDB / ID: 8qx2
TitleAplysia californica acetylcholine-binding protein in complex with racemic spiroimine (+)/(-)-4
ComponentsSoluble acetylcholine receptor
KeywordsCHOLINE-BINDING PROTEIN / ACHBP / complex / spiroimine / Aplysia californica
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion binding
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
Similarity search - Domain/homology
: / ISOPROPYL ALCOHOL / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSulzenbacher, G. / Bourne, Y. / Marchot, P.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: Mar Drugs / Year: 2024
Title: The Cyclic Imine Core Common to the Marine Macrocyclic Toxins Is Sufficient to Dictate Nicotinic Acetylcholine Receptor Antagonism.
Authors: Bourne, Y. / Sulzenbacher, G. / Chabaud, L. / Araoz, R. / Radic, Z. / Conrod, S. / Taylor, P. / Guillou, C. / Molgo, J. / Marchot, P.
History
DepositionOct 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Structure summary / Category: citation / struct / Item: _citation.journal_volume / _struct.title
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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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)124,81411
Polymers123,6375
Non-polymers1,1776
Water9,368520
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-57 kcal/mol
Surface area45520 Å2
Unit cell
Length a, b, c (Å)75.787, 123.632, 131.103
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: 24727.484 Da / Num. of mol.: 5 / Fragment: UNP residues 18-225
Source method: isolated from a genetically manipulated source
Details: ...Details: DYKDDDDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): HEK293S GnTI / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-ILR / Spiroimine (+)-4 R / (6~{R})-7-methyl-1,4-dioxa-8-azadispiro[4.0.5^{6}.4^{5}]pentadec-7-ene / (R)-(+)-Spiroimine


Mass: 223.311 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H21NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10% polyethylene glycol 1500 (w/v), 0.1 M sodium citrate buffer pH 5.5, 24% isopropanol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9708 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9708 Å / Relative weight: 1
ReflectionResolution: 2.1→65.61 Å / Num. obs: 72272 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.065 / Rrim(I) all: 0.128 / Χ2: 0.85 / Net I/σ(I): 8.7 / Num. measured all: 253219
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.614 / Num. measured all: 15594 / Num. unique obs: 4374 / CC1/2: 0.687 / Rpim(I) all: 0.369 / Rrim(I) all: 0.72 / Χ2: 0.73 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→64.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.734 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20966 2180 3 %RANDOM
Rwork0.17881 ---
obs0.17976 70046 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.68 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---1.78 Å20 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.1→64.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8597 0 0 520 9117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128870
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168039
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.6812113
X-RAY DIFFRACTIONr_angle_other_deg0.4311.618593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11251074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.897553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.736101436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.21339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022032
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_it2.0022.4854272
X-RAY DIFFRACTIONr_mcbond_other2.0012.4854272
X-RAY DIFFRACTIONr_mcangle_it3.2364.4525333
X-RAY DIFFRACTIONr_mcangle_other3.2364.4535334
X-RAY DIFFRACTIONr_scbond_it3.0972.924598
X-RAY DIFFRACTIONr_scbond_other3.0972.924598
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9195.1916774
X-RAY DIFFRACTIONr_long_range_B_refined7.27126.069531
X-RAY DIFFRACTIONr_long_range_B_other7.23925.849440
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 148 -
Rwork0.254 5108 -
obs--99.96 %
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)
11.0005-0.1022-0.4731.24040.04841.10810.05220.0150.0925-0.0080.0019-0.2382-0.01730.0774-0.05410.0081-0.005-0.0080.0170.01610.084458.2273-3.19571.935
21.08520.230.12550.8646-0.01920.8691-0.03170.1295-0.142-0.04330.0397-0.134-0.00250.0634-0.0080.01990.00330.02340.022-0.00950.07841.8154-22.1331-4.1872
30.5594-0.1872-0.15640.73050.22691.2751-0.03770.0572-0.1056-0.02-0.08030.2308-0.0362-0.06120.1180.01-0.0048-0.00090.0309-0.04020.092216.6861-12.2274-5.3703
40.6490.19130.21260.6150.21270.6879-0.05580.03640.0626-0.0537-0.02020.165-0.10530.00390.07590.06040.0227-0.01490.0225-0.01370.064518.469113.9565-1.4905
51.02080.2739-0.25460.9372-0.37040.8791-0.05230.0040.1061-0.01860.0427-0.0834-0.0342-0.03110.00960.0808-0.0124-0.00680.0071-0.0130.054944.55320.17963.9515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 208
2X-RAY DIFFRACTION2B-8 - 208
3X-RAY DIFFRACTION3C-5 - 208
4X-RAY DIFFRACTION4D-8 - 208
5X-RAY DIFFRACTION5E-3 - 207

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