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- PDB-5sxv: X-ray structure of 2-bromoethanol bound to a pentameric ligand ga... -

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Basic information

Entry
Database: PDB / ID: 5sxv
TitleX-ray structure of 2-bromoethanol bound to a pentameric ligand gated ion channel (ELIC) in a resting state
ComponentsCys-loop ligand-gated ion channel
KeywordsTRANSPORT PROTEIN / ELIC / anesthetic / ethanol / resting state
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
2-BROMOETHANOL / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsChen, Q. / Kinde, M. / Cohen, A. / Xu, Y. / Tang, P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM066358 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM056257 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM075770 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM049202 United States
CitationJournal: Structure / Year: 2017
Title: Structural Basis of Alcohol Inhibition of the Pentameric Ligand-Gated Ion Channel ELIC.
Authors: Chen, Q. / Wells, M.M. / Tillman, T.S. / Kinde, M.N. / Cohen, A. / Xu, Y. / Tang, P.
History
DepositionAug 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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)374,74152
Polymers368,79010
Non-polymers5,95142
Water18010
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)187,37126
Polymers184,3955
Non-polymers2,97621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30790 Å2
ΔGint-161 kcal/mol
Surface area65500 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)187,37126
Polymers184,3955
Non-polymers2,97621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30880 Å2
ΔGint-161 kcal/mol
Surface area65530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.747, 266.935, 111.416
Angle α, β, γ (deg.)90.00, 107.04, 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: 36879.000 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Chemical...
ChemComp-BRJ / 2-BROMOETHANOL


Mass: 124.965 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H5BrO
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: PEG 4000, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9195 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 3.4→39.63 Å / Num. obs: 80765 / % possible obs: 99.9 % / Redundancy: 43.1 % / Net I/σ(I): 12.2
Reflection shellResolution: 3.4→3.47 Å / Redundancy: 36.9 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSJanuary 10, 2014 BUILT=20140307data scaling
Aimless0.1.26data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RQU

3rqu


Resolution: 3.4→29.735 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.65
RfactorNum. reflection% reflection
Rfree0.2588 8072 5.06 %
Rwork0.215 --
obs0.2172 80599 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→29.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25160 0 248 10 25418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326056
X-RAY DIFFRACTIONf_angle_d0.84335444
X-RAY DIFFRACTIONf_dihedral_angle_d12.6949412
X-RAY DIFFRACTIONf_chiral_restr0.0343910
X-RAY DIFFRACTIONf_plane_restr0.0044500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43860.40852530.36724907X-RAY DIFFRACTION98
3.4386-3.4790.36722560.35645049X-RAY DIFFRACTION99
3.479-3.52130.37022620.34514986X-RAY DIFFRACTION100
3.5213-3.56580.37392790.32685118X-RAY DIFFRACTION100
3.5658-3.61270.33482740.32625059X-RAY DIFFRACTION100
3.6127-3.66210.36513130.3165020X-RAY DIFFRACTION100
3.6621-3.71430.32582700.30035081X-RAY DIFFRACTION100
3.7143-3.76960.35592630.29155006X-RAY DIFFRACTION100
3.7696-3.82840.30582580.285083X-RAY DIFFRACTION100
3.8284-3.89110.31362360.26615120X-RAY DIFFRACTION100
3.8911-3.9580.26892810.26185052X-RAY DIFFRACTION100
3.958-4.02980.34562560.25365055X-RAY DIFFRACTION100
4.0298-4.10710.27122510.24445100X-RAY DIFFRACTION100
4.1071-4.19070.30212620.23285067X-RAY DIFFRACTION100
4.1907-4.28160.25342800.21695043X-RAY DIFFRACTION100
4.2816-4.38090.23762770.20675036X-RAY DIFFRACTION100
4.3809-4.49010.23322830.19585065X-RAY DIFFRACTION100
4.4901-4.61110.27242530.18825144X-RAY DIFFRACTION100
4.6111-4.74620.22552580.18084997X-RAY DIFFRACTION100
4.7462-4.89880.24012230.1915125X-RAY DIFFRACTION100
4.8988-5.0730.28032950.20255004X-RAY DIFFRACTION99
5.073-5.27510.2362590.19095084X-RAY DIFFRACTION100
5.2751-5.51370.22952740.20085019X-RAY DIFFRACTION100
5.5137-5.80240.22872900.19735086X-RAY DIFFRACTION100
5.8024-6.16290.24852920.18655069X-RAY DIFFRACTION100
6.1629-6.63390.26032990.20065005X-RAY DIFFRACTION100
6.6339-7.29250.24322720.19965015X-RAY DIFFRACTION100
7.2925-8.32750.20652780.17385071X-RAY DIFFRACTION100
8.3275-10.41620.15892690.13395024X-RAY DIFFRACTION99
10.4162-29.73640.26522560.21045038X-RAY DIFFRACTION99

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