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- PDB-8q1t: X-ray structure of acetylcholine binding protein (AChBP) in compl... -

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Basic information

Entry
Database: PDB / ID: 8q1t
TitleX-ray structure of acetylcholine binding protein (AChBP) in complex with IOTA739
ComponentsAcetylcholine-binding protein
KeywordsCHOLINE-BINDING PROTEIN / Acetylcholine binding protein / ligand gated ion channel / SPR
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / neuron projection / 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
1,10-PHENANTHROLINE / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCederfelt, D. / Lund, B.A. / Boronat, P. / Hennig, S. / Dobritzsch, D. / 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. / Hennig, S. / Lund, B.A. / Zara, L. / Dobritzsch, D. / de Esch, I.J.P. / Danielson, U.H.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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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)235,77719
Polymers234,20010
Non-polymers1,5779
Water3,153175
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)118,12410
Polymers117,1005
Non-polymers1,0245
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint-33 kcal/mol
Surface area42740 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)117,6539
Polymers117,1005
Non-polymers5534
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-75 kcal/mol
Surface area40870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.950, 117.850, 239.750
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
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 23420.014 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: 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.: 3
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
#3: Chemical
ChemComp-PHN / 1,10-PHENANTHROLINE


Mass: 180.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350 3% Ammonium sulfate 1.8 M 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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→49.6 Å / Num. obs: 43398 / % possible obs: 99.83 % / Redundancy: 7.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.2174 / Net I/σ(I): 8.28
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.906 / Num. unique obs: 31167 / CC1/2: 0.523

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.6 Å / Cor.coef. Fo:Fc: 0.93 / SU B: 25.771 / SU ML: 0.357 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rwork0.2302 ---
obs0.2302 43393 99.93 %-
Rfree---RANDOM
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.157 Å2
Baniso -1Baniso -2Baniso -3
1-9.74 Å20 Å20 Å2
2---4.48 Å20 Å2
3----5.26 Å2
Refinement stepCycle: 1 / Resolution: 3→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16208 0 10 175 16393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01216597
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615231
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.6622656
X-RAY DIFFRACTIONr_angle_other_deg0.4481.58135103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.10451994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.7245131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.187102725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.22591
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023865
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_it9.5238.8488036
X-RAY DIFFRACTIONr_mcbond_other9.528.8488036
X-RAY DIFFRACTIONr_mcangle_it14.97815.89710010
X-RAY DIFFRACTIONr_mcangle_other14.97815.89610011
X-RAY DIFFRACTIONr_scbond_it9.2769.4078561
X-RAY DIFFRACTIONr_scbond_other9.2529.3948554
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.68717.0412635
X-RAY DIFFRACTIONr_long_range_B_refined22.458107.966328
X-RAY DIFFRACTIONr_long_range_B_other22.439107.9166313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.453 3119 -
obs--99.94 %

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