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

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Basic information

Entry
Database: PDB / ID: 5sxu
TitleX-ray structure of 2-bromoethanol bound to a pentameric ligand gated ion channel (ELIC) in a desensitized state
ComponentsGamma-aminobutyric-acid receptor subunit beta-1
KeywordsPROTEIN TRANSPORT / ELIC / anesthetic / ethanol / desensitized state
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / 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
3-AMINOPROPANE / 2-BROMOETHANOL / Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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: 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)375,40364
Polymers368,79010
Non-polymers6,61354
Water543
1
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,70232
Polymers184,3955
Non-polymers3,30727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32330 Å2
ΔGint-174 kcal/mol
Surface area64850 Å2
MethodPISA
2
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)187,70232
Polymers184,3955
Non-polymers3,30727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32230 Å2
ΔGint-170 kcal/mol
Surface area65300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.903, 266.791, 111.109
Angle α, β, γ (deg.)90.00, 107.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

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


Mass: 36879.000 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 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4

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Non-polymers , 5 types, 57 molecules

#2: Chemical...
ChemComp-BRJ / 2-BROMOETHANOL


Mass: 124.965 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H5BrO
#3: Chemical
ChemComp-3CN / 3-AMINOPROPANE


Mass: 59.110 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H9N
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.07 Å3/Da / Density % sol: 69.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: PEG 4000, ammonium sulfate, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID

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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: 3.07→39.61 Å / Num. obs: 109403 / % possible obs: 99.9 % / Redundancy: 36.4 % / Net I/σ(I): 19.1
Reflection shellResolution: 3.07→3.12 Å / Redundancy: 37.3 % / Mean I/σ(I) obs: 1 / % possible all: 100

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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: 3.1→29.927 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 28.51
RfactorNum. reflection% reflection
Rfree0.2387 10299 4.9 %
Rwork0.1996 --
obs0.2016 106078 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25160 0 290 3 25453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626086
X-RAY DIFFRACTIONf_angle_d1.32835464
X-RAY DIFFRACTIONf_dihedral_angle_d14.1379422
X-RAY DIFFRACTIONf_chiral_restr0.0533910
X-RAY DIFFRACTIONf_plane_restr0.0074500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13520.35293160.3536632X-RAY DIFFRACTION99
3.1352-3.17210.37183660.3326674X-RAY DIFFRACTION100
3.1721-3.21070.34293440.32916682X-RAY DIFFRACTION100
3.2107-3.25130.38953080.32436604X-RAY DIFFRACTION100
3.2513-3.2940.34553710.31836672X-RAY DIFFRACTION100
3.294-3.33910.34443360.29946640X-RAY DIFFRACTION100
3.3391-3.38670.31913430.29126646X-RAY DIFFRACTION100
3.3867-3.43720.33573510.28196648X-RAY DIFFRACTION100
3.4372-3.49080.30133760.25996690X-RAY DIFFRACTION100
3.4908-3.5480.29333380.2456640X-RAY DIFFRACTION100
3.548-3.60910.30333240.24636668X-RAY DIFFRACTION100
3.6091-3.67460.30993460.23896719X-RAY DIFFRACTION100
3.6746-3.74510.30173120.23556689X-RAY DIFFRACTION100
3.7451-3.82140.28743940.23336646X-RAY DIFFRACTION100
3.8214-3.90430.26513490.20676665X-RAY DIFFRACTION100
3.9043-3.9950.26293010.20816714X-RAY DIFFRACTION100
3.995-4.09460.26713130.20866691X-RAY DIFFRACTION100
4.0946-4.2050.21683280.19236656X-RAY DIFFRACTION100
4.205-4.32840.21893270.1756713X-RAY DIFFRACTION100
4.3284-4.46770.21763680.16196670X-RAY DIFFRACTION100
4.4677-4.62680.21043150.16566778X-RAY DIFFRACTION100
4.6268-4.81130.2033100.16026674X-RAY DIFFRACTION100
4.8113-5.02930.21782810.17016748X-RAY DIFFRACTION100
5.0293-5.29310.20983710.17026673X-RAY DIFFRACTION100
5.2931-5.62270.21614070.17666587X-RAY DIFFRACTION100
5.6227-6.05350.21194150.17596537X-RAY DIFFRACTION100
6.0535-6.65670.24013570.19026692X-RAY DIFFRACTION100
6.6567-7.60610.20383580.18076696X-RAY DIFFRACTION100
7.6061-9.53120.15493390.14316647X-RAY DIFFRACTION100
9.5312-29.92820.25283350.21666639X-RAY DIFFRACTION99

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