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- PDB-4z91: ELIC cocrystallized with isofluorane in a desensitized state -

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Basic information

Entry
Database: PDB / ID: 4z91
TitleELIC cocrystallized with isofluorane in a desensitized state
ComponentsGamma-aminobutyric-acid receptor subunit beta-1
KeywordsTRANSPORT PROTEIN / ELIC / isoflurane / anesthetics / desensitized state
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-4LE / 1.7.6 3-bromanylpropan-1-amine / Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3915 Å
AuthorsChen, Q. / Kinde, M.N. / Arjunan, P. / 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)R01GM056257 United States
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)R37GM049202 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM075770 United States
CitationJournal: Sci Rep / Year: 2015
Title: Direct Pore Binding as a Mechanism for Isoflurane Inhibition of the Pentameric Ligand-gated Ion Channel ELIC.
Authors: Chen, Q. / Kinde, M.N. / Arjunan, P. / Wells, M.M. / Cohen, A.E. / Xu, Y. / Tang, P.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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)374,24044
Polymers368,79010
Non-polymers5,45034
Water1,45981
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)187,12022
Polymers184,3955
Non-polymers2,72517
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27140 Å2
ΔGint-129 kcal/mol
Surface area66730 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)187,12022
Polymers184,3955
Non-polymers2,72517
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27660 Å2
ΔGint-131 kcal/mol
Surface area66710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.761, 267.595, 111.368
Angle α, β, γ (deg.)90.00, 107.80, 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: 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
#2: Chemical
ChemComp-4LE / (2R)-2-chloro-2-(difluoromethoxy)-1,1,1-trifluoroethane


Mass: 184.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2ClF5O
#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: Chemical
ChemComp-4LJ / 1.7.6 3-bromanylpropan-1-amine


Mass: 138.006 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8BrN
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 4.1 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: isoflurane, 3-bromopropylamine, PEG 4000, ammonium sulphate, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9199 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 3.39→40.01 Å / Num. obs: 156498 / % possible obs: 98.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 12.2
Reflection shellResolution: 3.39→3.46 Å / Redundancy: 6.6 % / % possible all: 91.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.9_1692refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RQU

3rqu


Resolution: 3.3915→34.893 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.88 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 3986 2.55 %Random selection
Rwork0.1923 ---
obs0.1938 156498 97.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3915→34.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25270 0 180 81 25531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01126106
X-RAY DIFFRACTIONf_angle_d1.4335572
X-RAY DIFFRACTIONf_dihedral_angle_d13.8469444
X-RAY DIFFRACTIONf_chiral_restr0.0643924
X-RAY DIFFRACTIONf_plane_restr0.0074520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3915-3.43280.41331030.33874457X-RAY DIFFRACTION79
3.4328-3.47620.3771660.32585444X-RAY DIFFRACTION97
3.4762-3.52190.30741440.31815483X-RAY DIFFRACTION98
3.5219-3.57010.31061400.30915470X-RAY DIFFRACTION98
3.5701-3.62110.41541340.31365469X-RAY DIFFRACTION98
3.6211-3.67510.3621700.31315410X-RAY DIFFRACTION97
3.6751-3.73250.36771380.30675333X-RAY DIFFRACTION95
3.7325-3.79360.38391210.29165329X-RAY DIFFRACTION95
3.7936-3.85890.30031490.25385156X-RAY DIFFRACTION92
3.8589-3.9290.35671250.2495314X-RAY DIFFRACTION95
3.929-4.00450.28841500.23745598X-RAY DIFFRACTION99
4.0045-4.08610.28281440.22085550X-RAY DIFFRACTION100
4.0861-4.17480.23831500.19295563X-RAY DIFFRACTION100
4.1748-4.27170.28311380.19445608X-RAY DIFFRACTION99
4.2717-4.37840.20391420.17335551X-RAY DIFFRACTION99
4.3784-4.49650.21931500.15715557X-RAY DIFFRACTION99
4.4965-4.62850.19321450.14625587X-RAY DIFFRACTION99
4.6285-4.77760.1851470.14145540X-RAY DIFFRACTION99
4.7776-4.94790.20081390.14975493X-RAY DIFFRACTION99
4.9479-5.14540.25661490.1475566X-RAY DIFFRACTION99
5.1454-5.37870.21011340.14585537X-RAY DIFFRACTION99
5.3787-5.66120.2051470.14795510X-RAY DIFFRACTION99
5.6612-6.01420.19661510.14725527X-RAY DIFFRACTION99
6.0142-6.47580.27691360.1645564X-RAY DIFFRACTION99
6.4758-7.12250.24151430.17365568X-RAY DIFFRACTION99
7.1225-8.14170.20771370.15045190X-RAY DIFFRACTION93
8.1417-10.21490.17521470.14415601X-RAY DIFFRACTION100
10.2149-34.89480.25791470.22975537X-RAY DIFFRACTION99

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