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- PDB-8q1m: Aplysia californica acetylcholine-binding protein in complex with... -

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Basic information

Entry
Database: PDB / ID: 8q1m
TitleAplysia californica acetylcholine-binding protein in complex with Spiroimine (+)-4 R
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 / identical protein binding / metal ion binding / 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
Similarity search - Domain/homology
: / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJul 31, 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 23, 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)125,90117
Polymers123,6375
Non-polymers2,26412
Water14,124784
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15350 Å2
ΔGint-108 kcal/mol
Surface area45180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.977, 114.995, 129.956
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 , 1 types, 5 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: SENSORY CELL / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8

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Sugars , 2 types, 2 molecules

#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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 794 molecules

#3: 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
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.66 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 17% polyethylene glycol 4K (w/v), 0.1 M TRIS-HCL pH 7.5, 0.2 M sodium citrate pH 6.0, 10% glycerol 10% (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→48.18 Å / Num. obs: 89606 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Χ2: 0.69 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.04 Å / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.878 / Num. measured all: 27930 / Num. unique obs: 4509 / CC1/2: 0.699 / Rpim(I) all: 0.383 / Rrim(I) all: 0.959 / Χ2: 0.73 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.835 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20604 4537 5.1 %RANDOM
Rwork0.1712 ---
obs0.17295 84991 99.92 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.431 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0 Å2
2---0.63 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 2→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8393 0 149 784 9326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138927
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178095
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.67612224
X-RAY DIFFRACTIONr_angle_other_deg1.3041.6118757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06551089
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93922.772469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.663151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.071552
X-RAY DIFFRACTIONr_chiral_restr0.0640.21197
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022045
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_it2.6762.6324275
X-RAY DIFFRACTIONr_mcbond_other2.6762.6324274
X-RAY DIFFRACTIONr_mcangle_it3.7893.925355
X-RAY DIFFRACTIONr_mcangle_other3.7893.925356
X-RAY DIFFRACTIONr_scbond_it3.6033.0944652
X-RAY DIFFRACTIONr_scbond_other3.6023.0944653
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3784.4946858
X-RAY DIFFRACTIONr_long_range_B_refined7.2632.2249929
X-RAY DIFFRACTIONr_long_range_B_other7.26631.7559735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 317 -
Rwork0.238 6197 -
obs--99.75 %
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)
10.6625-0.0308-0.03090.6250.12780.90960.01880.0175-0.1-0.041-0.0122-0.0959-0.00750.0505-0.00660.01420.0005-0.0030.00930.01220.062143.4834-22.7715-4.6331
20.2348-0.0311-0.02230.4764-0.03391.50980.00270.0052-0.0501-0.0514-0.00750.1411-0.0037-0.04860.00480.0081-0.0026-0.02020.02470.00070.059319.1994-11.5364-6.4744
30.47820.17710.09030.32450.10260.6619-0.07860.00510.0806-0.05580.00130.1415-0.10230.03430.07730.06730.0121-0.03610.009-0.00040.064721.901814.0354-3.4792
40.57480.2361-0.42610.6873-0.38651.90380.0068-0.01250.0738-0.04220.05420.0047-0.16820.0624-0.0610.0773-0.0377-0.00260.021-0.00160.011848.243919.40762.6417
50.18230.0378-0.07380.55140.2230.5622-0.016-0.0605-0.007-0.04580.0673-0.1518-0.05060.1105-0.05130.0102-0.01370.00670.0688-0.00090.052261.2126-3.87270.5997
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 208
2X-RAY DIFFRACTION2B-1 - 207
3X-RAY DIFFRACTION3C-8 - 207
4X-RAY DIFFRACTION4D-1 - 208
5X-RAY DIFFRACTION5E-2 - 207

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