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- PDB-9qm8: X-ray structure of acetylcholine binding protein (AChBP) in compl... -

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Basic information

Entry
Database: PDB / ID: 9qm8
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


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / 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
DepositionMar 22, 2025Deposition site: PDBE / Processing site: PDBE
SupersessionMay 21, 2025ID: 8Q1T
Revision 1.0May 21, 2025Provider: 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 area14130 Å2
ΔGint-31 kcal/mol
Surface area42780 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 area14110 Å2
ΔGint-74 kcal/mol
Surface area40990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.950, 117.850, 239.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 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
#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: obtained synthetically / 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
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: 2.26 Å3/Da / Density % sol: 45.59 %
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→49.59 Å / Num. obs: 43398 / % possible obs: 99.89 % / Redundancy: 7.5 % / Biso Wilson estimate: 78.11 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2174 / Rrim(I) all: 0.2334 / Net I/σ(I): 8.28
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.906 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 4269 / CC1/2: 0.523 / Rrim(I) all: 2.052 / % possible all: 99.93

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.59 Å / SU ML: 0.5139 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.4501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 1999 4.61 %
Rwork0.2243 41374 -
obs0.2255 43398 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.84 Å2
Refinement stepCycle: LAST / Resolution: 3→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16110 0 108 175 16393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011116574
X-RAY DIFFRACTIONf_angle_d1.301722607
X-RAY DIFFRACTIONf_chiral_restr0.07252589
X-RAY DIFFRACTIONf_plane_restr0.01192903
X-RAY DIFFRACTIONf_dihedral_angle_d8.73692213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.42861390.44932882X-RAY DIFFRACTION99.9
3.08-3.160.39861410.40142915X-RAY DIFFRACTION99.97
3.16-3.250.40951420.37952935X-RAY DIFFRACTION99.97
3.25-3.360.35331400.34842891X-RAY DIFFRACTION99.97
3.36-3.480.31911410.32352921X-RAY DIFFRACTION99.84
3.48-3.620.33191410.27642915X-RAY DIFFRACTION100
3.62-3.780.27851420.22152946X-RAY DIFFRACTION99.9
3.78-3.980.22271420.20452942X-RAY DIFFRACTION99.97
3.98-4.230.23921420.20152936X-RAY DIFFRACTION100
4.23-4.550.19021420.15252950X-RAY DIFFRACTION100
4.55-5.010.19561440.15452980X-RAY DIFFRACTION100
5.01-5.740.20061450.14382985X-RAY DIFFRACTION100
5.74-7.220.18961450.19563009X-RAY DIFFRACTION99.97
7.22-49.590.23911530.20973167X-RAY DIFFRACTION99.46

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