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- PDB-4twf: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 4twf
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromomemantine
ComponentsCys-loop ligand-gated ion channel
KeywordsTRANSPORT PROTEIN / ELIC / LGIC / cys-loop / channel / memantine / pore blocker
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma 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
Bromomemantine / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.901 Å
AuthorsUlens, C. / Spurny, R. / Thompson, A.J. / Alqazzaz, M. / Debaveye, S. / Lu, H. / Price, K. / Villalgordo, J.M. / Tresadern, G. / Lynch, J.W. / Lummis, S.C.R.
CitationJournal: Structure / Year: 2014
Title: The Prokaryote Ligand-Gated Ion Channel ELIC Captured in a Pore Blocker-Bound Conformation by the Alzheimer's Disease Drug Memantine.
Authors: Ulens, C. / Spurny, R. / Thompson, A.J. / Alqazzaz, M. / Debaveye, S. / Han, L. / Price, K. / Villalgordo, J.M. / Tresadern, G. / Lynch, J.W. / Lummis, S.C.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel
F: Cys-loop ligand-gated ion channel
G: Cys-loop ligand-gated ion channel
H: Cys-loop ligand-gated ion channel
I: Cys-loop ligand-gated ion channel
J: Cys-loop ligand-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,91022
Polymers352,81210
Non-polymers3,09812
Water00
1
A: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,95511
Polymers176,4065
Non-polymers1,5496
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25310 Å2
ΔGint-147 kcal/mol
Surface area66810 Å2
MethodPISA
2
F: Cys-loop ligand-gated ion channel
G: Cys-loop ligand-gated ion channel
H: Cys-loop ligand-gated ion channel
I: Cys-loop ligand-gated ion channel
J: Cys-loop ligand-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,95511
Polymers176,4065
Non-polymers1,5496
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26030 Å2
ΔGint-145 kcal/mol
Surface area65540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.505, 266.092, 112.175
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cys-loop ligand-gated ion channel / ELIC


Mass: 35281.191 Da / Num. of mol.: 10 / Fragment: UNP residues 11-316 / Mutation: F246S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Chemical
ChemComp-BR7 / Bromomemantine


Mass: 258.198 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H20BrN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulphate, 50 mM ADA pH 5.5, 20 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91946 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91946 Å / Relative weight: 1
ReflectionResolution: 3.9→49.83 Å / Num. obs: 53624 / % possible obs: 99.3 % / Redundancy: 4.9 % / Net I/σ(I): 8.7
Reflection shellResolution: 3.9→4.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.936 / Num. unique all: 7432 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vl0

2vl0


Resolution: 3.901→49.83 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 2718 5.08 %
Rwork0.2021 --
obs0.2045 53548 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.901→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24970 0 168 0 25138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925832
X-RAY DIFFRACTIONf_angle_d1.5635310
X-RAY DIFFRACTIONf_dihedral_angle_d15.5489200
X-RAY DIFFRACTIONf_chiral_restr0.0663938
X-RAY DIFFRACTIONf_plane_restr0.0084460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9014-3.97240.38491330.31862320X-RAY DIFFRACTION87
3.9724-4.04870.37131370.28052708X-RAY DIFFRACTION100
4.0487-4.13130.2751400.25312681X-RAY DIFFRACTION100
4.1313-4.22110.31841380.23952688X-RAY DIFFRACTION100
4.2211-4.31930.26131440.21432708X-RAY DIFFRACTION100
4.3193-4.42720.27741520.20882664X-RAY DIFFRACTION100
4.4272-4.54680.2231300.18792681X-RAY DIFFRACTION100
4.5468-4.68050.26041480.18282708X-RAY DIFFRACTION100
4.6805-4.83150.24511380.17572709X-RAY DIFFRACTION100
4.8315-5.0040.21981260.18332691X-RAY DIFFRACTION100
5.004-5.20420.27441470.17532689X-RAY DIFFRACTION100
5.2042-5.44070.21111500.17772692X-RAY DIFFRACTION100
5.4407-5.72720.23181420.17562684X-RAY DIFFRACTION100
5.7272-6.08540.25981460.182700X-RAY DIFFRACTION100
6.0854-6.55440.28311690.19942683X-RAY DIFFRACTION100
6.5544-7.21220.25861560.19212688X-RAY DIFFRACTION100
7.2122-8.25170.21911550.17892692X-RAY DIFFRACTION100
8.2517-10.38080.18271480.16132697X-RAY DIFFRACTION100
10.3808-49.8380.25971190.24882747X-RAY DIFFRACTION99
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)
10.57120.17950.05392.66152.62866.986-0.1232-0.2463-0.17810.6742-0.20350.8790.7003-0.56770.05070.7798-0.08040.06360.89210.04640.9341-125.4088-49.3244-44.9559
20.5501-0.36120.13992.75192.20745.8036-0.0723-0.0896-0.12840.19180.1071-0.02380.15620.11240.03650.91760.01570.12040.524-0.00750.8188-104.8676-61.078-40.8497
31.16570.09-2.06580.8780.46297.795-0.056-0.1003-0.1302-0.05990.1143-0.60480.61290.4547-0.39030.78860.19470.03990.53750.02970.9136-86.6207-45.6265-43.1651
41.1055-0.3035-0.07380.9811.0917.00750.1309-0.20580.2277-0.1081-0.071-0.35870.66260.1326-0.42451.04740.0240.34720.6874-0.00270.9047-95.8336-23.8998-48.5591
50.9173-0.08610.76141.70310.83628.2203-0.0890.08550.12080.0085-0.00870.2791-0.8853-0.14910.12460.8350.11210.13760.83260.24010.6734-119.9088-26.2105-49.6554
68.13981.6283-0.35251.38170.0011.15380.102-0.75110.59050.577-0.1459-0.15590.0556-0.12290.14820.89520.02480.11550.7916-0.03631.0968-82.4367-117.4683-18.2874
76.61292.73030.67452.01150.45670.7601-0.24760.204-0.5336-0.18770.1798-0.25190.18010.23170.13310.97170.03330.26540.6113-0.01960.903-78.7936-127.9923-39.7293
87.26420.00951.74671.3789-0.12781.06510.05620.6679-0.5935-0.29250.0831-0.33170.01730.34460.03821.0464-0.07390.20170.5426-0.1831.1167-81.6389-111.5497-57.0961
97.43811.92980.18260.84830.24231.1296-0.3116-0.0328-1.0093-0.36290.2485-0.5162-0.27370.1460.25480.86-0.02370.04320.5584-0.03351.1724-86.984-90.4402-46.3546
105.72120.1666-0.57031.3004-0.34240.9403-0.1055-0.58060.5960.52010.0570.072-0.10340.01840.0090.78940.1421-0.0030.815-0.24811.2423-87.5996-94.2477-22.402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J

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