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- PDB-5lg3: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 5lg3
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with chlorpromazine
ComponentsGamma-aminobutyric-acid receptor subunit beta-1
KeywordsTRANSPORT PROTEIN / Ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-Z80 / Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.567 Å
AuthorsNys, M. / Wijckmans, E. / Farinha, A. / Brams, M. / Spurny, R. / Ulens, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine.
Authors: Nys, M. / Wijckmans, E. / Farinha, A. / Yoluk, O. / Andersson, M. / Brams, M. / Spurny, R. / Peigneur, S. / Tytgat, J. / Lindahl, E. / Ulens, C.
History
DepositionJul 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 7, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: 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: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,02220
Polymers353,83410
Non-polymers3,18910
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50910 Å2
ΔGint-296 kcal/mol
Surface area128340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.200, 266.650, 111.040
Angle α, β, γ (deg.)90.00, 107.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gamma-aminobutyric-acid receptor subunit beta-1


Mass: 35383.367 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria)
Strain: 3937 / Gene: Dda3937_00520 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4
#2: Chemical
ChemComp-Z80 / 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine / Chlorpromazine


Mass: 318.864 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C17H19ClN2S

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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: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulfate 50 mM ADA (N-(2-acetamido)iminodiacetic acid) pH 6.5 9-12 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.4→49.16 Å / Num. obs: 67372 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.8
Reflection shellRmerge(I) obs: 0.0371

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4a97

4a97


Resolution: 3.567→44.746 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.2531 3412 5.06 %
Rwork0.22 --
obs0.2217 67372 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.567→44.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25045 0 210 0 25255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00525954
X-RAY DIFFRACTIONf_angle_d0.93335381
X-RAY DIFFRACTIONf_dihedral_angle_d16.14115083
X-RAY DIFFRACTIONf_chiral_restr0.0523899
X-RAY DIFFRACTIONf_plane_restr0.0054489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5674-3.61830.37441070.35311944X-RAY DIFFRACTION71
3.6183-3.67230.40341430.36192621X-RAY DIFFRACTION98
3.6723-3.72970.33741490.30982693X-RAY DIFFRACTION98
3.7297-3.79080.32431370.29232707X-RAY DIFFRACTION98
3.7908-3.85610.30451400.28332702X-RAY DIFFRACTION99
3.8561-3.92620.35391430.31082635X-RAY DIFFRACTION97
3.9262-4.00170.30461410.2592690X-RAY DIFFRACTION99
4.0017-4.08330.24481560.2362674X-RAY DIFFRACTION99
4.0833-4.1720.27281400.22332677X-RAY DIFFRACTION99
4.172-4.2690.25511290.21412742X-RAY DIFFRACTION99
4.269-4.37570.20481430.20332688X-RAY DIFFRACTION99
4.3757-4.49390.24051270.19222703X-RAY DIFFRACTION99
4.4939-4.6260.20721480.1782725X-RAY DIFFRACTION99
4.626-4.77510.19621310.16062695X-RAY DIFFRACTION99
4.7751-4.94560.18421430.17052685X-RAY DIFFRACTION99
4.9456-5.14330.20821470.16922708X-RAY DIFFRACTION99
5.1433-5.3770.20721640.17832671X-RAY DIFFRACTION99
5.377-5.660.22511520.18762708X-RAY DIFFRACTION99
5.66-6.01380.21711520.1982709X-RAY DIFFRACTION99
6.0138-6.47690.24611440.21082728X-RAY DIFFRACTION99
6.4769-7.12630.28451410.22522694X-RAY DIFFRACTION99
7.1263-8.15210.24951510.21092728X-RAY DIFFRACTION99
8.1521-10.25040.20481500.17742722X-RAY DIFFRACTION99
10.2504-44.7490.30161340.25632711X-RAY DIFFRACTION97

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