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- PDB-6sh0: Crystal structure of AcAChBP in complex with anatoxin -

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Basic information

Entry
Database: PDB / ID: 6sh0
TitleCrystal structure of AcAChBP in complex with anatoxin
ComponentsAcetylcholine binding protein
KeywordsSIGNALING PROTEIN / toxin / acetylcholine binding protein
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
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
Chem-4P0 / ACETATE ION / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHunter, W.N. / Dawson, A. / Parker, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Delineating the activity of the potent nicotinic acetylcholine receptor agonists (+)-anatoxin-a and (-)-hosieine-A
Authors: Parker, H.P. / Dawson, A. / Jones, M.J. / Yan, R. / Ouyang, J. / Hong, R. / Hunter, W.N.
History
DepositionAug 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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: 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)287,96244
Polymers283,26810
Non-polymers4,69434
Water17,240957
1
A: Acetylcholine binding protein
B: Acetylcholine binding protein
C: Acetylcholine binding protein
D: Acetylcholine binding protein
E: Acetylcholine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,11122
Polymers141,6345
Non-polymers2,47817
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16520 Å2
ΔGint-61 kcal/mol
Surface area42040 Å2
MethodPISA
2
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)143,85022
Polymers141,6345
Non-polymers2,21617
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16510 Å2
ΔGint-62 kcal/mol
Surface area42510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.968, 129.872, 131.322
Angle α, β, γ (deg.)90.000, 103.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 19 molecules ABCDEFGHIJ

#1: Protein
Acetylcholine binding protein


Mass: 28326.750 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8
#2: 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.: 9
Source method: isolated from a genetically manipulated source
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 , 4 types, 982 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-4P0 / 1-[(1R,6R)-9-azabicyclo[4.2.1]non-2-en-2-yl]ethanone


Mass: 165.232 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 957 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Reservoir solution: 8% PEG 4K, 0.1 M NaOAc pH 4.6 Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5, 4mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 15, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→127.87 Å / Num. obs: 119138 / % possible obs: 99.5 % / Redundancy: 11.8 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.089 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5811 / CC1/2: 0.813 / Rpim(I) all: 0.286 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xys

2xys


Resolution: 2.5→59.77 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.85 / SU B: 11.279 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.419 / ESU R Free: 0.292
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.289 6041 5.1 %RANDOM
Rwork0.2528 ---
obs0.2546 113033 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.47 Å2 / Biso mean: 26.137 Å2 / Biso min: 4.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å2-1.1 Å2
2--2.12 Å20 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 2.5→59.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16442 0 316 957 17715
Biso mean--42.51 23.46 -
Num. residues----2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0217238
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215316
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.96523528
X-RAY DIFFRACTIONr_angle_other_deg0.8423.00135686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2445.0152057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53224.45800
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.629152750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5451596
X-RAY DIFFRACTIONr_chiral_restr0.0640.22650
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02119075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023465
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 449 -
Rwork0.335 8327 -
all-8776 -
obs--99.99 %

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