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

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Basic information

Entry
Database: PDB / ID: 8qtl
TitleAplysia californica acetylcholine-binding protein in complex with Spiroimine (-)-4 S
ComponentsSoluble acetylcholine receptor
KeywordsCHOLINE-BINDING PROTEIN / ACHBP / complex / spiroimine / Aplysia californica
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
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 / FOURIER SYNTHESIS / Resolution: 1.85 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 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)125,77518
Polymers123,6375
Non-polymers2,13813
Water12,719706
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15320 Å2
ΔGint-119 kcal/mol
Surface area45460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.343, 116.032, 131.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 6 molecules ABCDE

#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
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): HEK293S GnTI / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 718 molecules

#3: Chemical
ChemComp-WSP / Spiroimine (-)-4 S / (6~{S})-7-methyl-1,4-dioxa-8-azadispiro[4.0.5^{6}.4^{5}]pentadec-7-ene / (S)-(-)-Spiroimine


Mass: 223.311 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H21NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 706 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15% polyethylene glycol 4K (w/v), 0.1 M HEPES pH 7.5, 10% isopropanol (v/v), 10% glycerol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.00882 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00882 Å / Relative weight: 1
ReflectionResolution: 1.85→48.49 Å / Num. obs: 109510 / % possible obs: 94.9 % / Redundancy: 7 % / Biso Wilson estimate: 32.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.026 / Rrim(I) all: 0.05 / Χ2: 1.02 / Net I/σ(I): 22.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5565 / CC1/2: 0.618 / Rpim(I) all: 0.575 / Rrim(I) all: 0.954 / Χ2: 1.01 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→47.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.898 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21144 5509 5 %RANDOM
Rwork0.18204 ---
obs0.18352 103900 94.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.662 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0 Å2
2---1.19 Å20 Å2
3---1.36 Å2
Refinement stepCycle: 1 / Resolution: 1.85→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8390 0 140 706 9236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138923
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178101
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.67412202
X-RAY DIFFRACTIONr_angle_other_deg1.3071.60818748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83451078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54722.746477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.592151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5481553
X-RAY DIFFRACTIONr_chiral_restr0.0610.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022048
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_it1.8372.9944264
X-RAY DIFFRACTIONr_mcbond_other1.8362.9944263
X-RAY DIFFRACTIONr_mcangle_it2.8054.4725325
X-RAY DIFFRACTIONr_mcangle_other2.8054.4725326
X-RAY DIFFRACTIONr_scbond_it2.5133.4544659
X-RAY DIFFRACTIONr_scbond_other2.5123.4544660
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9715.0556867
X-RAY DIFFRACTIONr_long_range_B_refined6.09236.1359725
X-RAY DIFFRACTIONr_long_range_B_other6.04635.629538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 434 -
Rwork0.282 7900 -
obs--98.74 %
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)
10.3103-0.0309-0.04840.81620.19420.55720.0022-0.0396-0.0247-0.05390.055-0.2565-0.05390.1071-0.05720.0096-0.02080.01480.0595-0.00540.086261.284-3.8810.333
20.8911-0.0519-0.25370.7490.20851.15230.01160.0547-0.1018-0.045-0.0023-0.11950.02150.0019-0.00940.01310.00360.0050.01260.00670.054643.384-23.049-4.415
30.5762-0.06040.19510.6589-0.13331.4986-0.00290.0214-0.1063-0.05190.03730.2195-0.0217-0.0519-0.03440.0061-0.0088-0.01840.03830.01450.088618.86-11.215-6.21
40.87130.22540.2290.46190.32060.4527-0.1553-0.00360.1354-0.09550.04410.1647-0.16960.04880.11120.11610.0171-0.04510.02990.00940.063722.00814.17-3.301
51.08660.3695-0.38430.8332-0.39281.5786-0.03840.01780.1231-0.06450.0686-0.0315-0.18350.0268-0.03020.116-0.0334-0.00490.0129-0.0030.022648.40419.4912.371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 207
2X-RAY DIFFRACTION2B-4 - 208
3X-RAY DIFFRACTION3C-2 - 207
4X-RAY DIFFRACTION4D-8 - 207
5X-RAY DIFFRACTION5E-1 - 208

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