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- PDB-7dji: Crystal structure of Lymnaea stagnalis Acetylcholine binding prot... -

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Basic information

Entry
Database: PDB / ID: 7dji
TitleCrystal structure of Lymnaea stagnalis Acetylcholine binding protein (AChBP) complexed with Paraherquamide A
ComponentsAcetylcholine-binding protein
KeywordsSIGNALING PROTEIN / Paraherquamide A / acetylcholine binding protein / nicotinic acetylcholine receptor
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
Paraherquamide A / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIhara, M. / Matsuda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H01472 Japan
CitationJournal: Mol.Pharmacol. / Year: 2023
Title: Determinants of subtype-selectivity of the anthelmintic paraherquamide A on Caenorhabditis elegans nicotinic acetylcholine receptors.
Authors: Koizumi, W. / Otsubo, S. / Furutani, S. / Niki, K. / Takayama, K. / Fujimura, S. / Maekawa, T. / Koyari, R. / Ihara, M. / Kai, K. / Hayashi, H. / Ali, M.S. / Kage-Nakadai, E. / Sattelle, D.B. / Matsuda, K.
History
DepositionNov 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,67815
Polymers121,1045
Non-polymers3,57410
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-32 kcal/mol
Surface area43850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.373, 74.373, 349.595
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Acetylcholine-binding protein / AchBP


Mass: 24220.826 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pPICZ alpha / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P58154
#2: Chemical
ChemComp-H8U / Paraherquamide A


Mass: 493.595 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C28H35N3O5
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.4 Å3/Da / Density % sol: 48.82 % / Description: Rod
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 14.1-15.6% PEG 4000, Sodium Citrate buffer pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 15, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.374 Å / Num. obs: 55263 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 21.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.713 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Mar 15, 2019 BUILT=20191211data processing
XDSVERSION Mar 15, 2019 BUILT=20191211data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZJU

2zju


Resolution: 2.2→47.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.842 / SU ML: 0.177 / Cross valid method: FREE R-VALUE / ESU R: 0.303 / ESU R Free: 0.214
Details: 1. HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS. 2. EXTRA H ATOM ON H8U IS PROTONATION OF TERT-AMINE.
RfactorNum. reflection% reflection
Rfree0.231 2734 4.959 %
Rwork0.185 --
obs-55135 99.9 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 49.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.565 Å20.282 Å20 Å2
2--0.565 Å20 Å2
3----1.832 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8176 0 250 486 8912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138678
X-RAY DIFFRACTIONr_bond_other_d0.0020.0187894
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.69611948
X-RAY DIFFRACTIONr_angle_other_deg1.151.62518169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48151027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39122.029478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.299151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6041569
X-RAY DIFFRACTIONr_chiral_restr0.0480.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021984
X-RAY DIFFRACTIONr_nbd_refined0.1690.21260
X-RAY DIFFRACTIONr_nbd_other0.1590.277
X-RAY DIFFRACTIONr_nbtor_refined0.1580.24109
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2514
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_it0.8723.1164105
X-RAY DIFFRACTIONr_mcbond_other0.8723.1164103
X-RAY DIFFRACTIONr_mcangle_it1.5714.675124
X-RAY DIFFRACTIONr_mcangle_other1.5714.675124
X-RAY DIFFRACTIONr_scbond_it0.7073.2094573
X-RAY DIFFRACTIONr_scbond_other0.7073.2094573
X-RAY DIFFRACTIONr_scangle_it1.2544.7736821
X-RAY DIFFRACTIONr_scangle_other1.2544.7736822
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 196 -
Rwork0.268 3906 -
obs--99.98 %
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)
11.32140.121-0.810.9250.36022.5874-0.085-0.0937-0.2803-0.0877-0.0216-0.17030.3560.08750.10660.16770.00610.07580.08180.01330.1039-35.1483-22.452517.8855
21.2251-0.4582-0.22522.0467-0.32223.2911-0.03660.1501-0.081-0.0956-0.010.24820.1118-0.3790.04660.0203-0.0476-0.00220.155-0.03130.0361-56.1929-6.192722.472
31.30030.45280.62720.92730.31792.75180.00210.15390.4096-0.09880.07520.1539-0.4126-0.176-0.07730.13440.01010.06280.17670.02650.181-47.155819.570923.3599
42.4681-0.1559-0.32691.4548-0.32173.1043-0.0211-0.01150.2279-0.17920.0539-0.1755-0.20840.1716-0.03280.1344-0.09280.07750.1549-0.05050.1218-20.439319.377719.7061
51.18460.3617-0.04472.11820.23263.0528-0.076-0.0773-0.142-0.19150.0393-0.5289-0.08910.38510.03670.09780.00370.12150.28410.02020.2317-13.1587-6.574316.3587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 205
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B1 - 206
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C1 - 205
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION4D1 - 205
8X-RAY DIFFRACTION4D401
9X-RAY DIFFRACTION5E1 - 205
10X-RAY DIFFRACTION5E401

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