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- PDB-5nkj: X-ray structure of the N239C mutant of GLIC -

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Basic information

Entry
Database: PDB / ID: 5nkj
TitleX-ray structure of the N239C mutant of GLIC
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / 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 / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
AuthorsHu, H. / Fourati, Z. / Delarue, M.
CitationJournal: Cell Rep / Year: 2018
Title: Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels.
Authors: Fourati, Z. / Howard, R.J. / Heusser, S.A. / Hu, H. / Ruza, R.R. / Sauguet, L. / Lindahl, E. / Delarue, M.
History
DepositionMar 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_validate_symm_contact ...diffrn_radiation_wavelength / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel


Theoretical massNumber of molelcules
Total (without water)181,3345
Polymers181,3345
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22460 Å2
ΔGint-153 kcal/mol
Surface area65210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.140, 134.690, 158.620
Angle α, β, γ (deg.)90.00, 99.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36266.762 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 44-359 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 5 Å3/Da / Density % sol: 75.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PH 4, VAPOR DIFFUSION, TEMPERATURE 293K / PH range: 4

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2017
RadiationMonochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→44.21 Å / Num. obs: 58339 / % possible obs: 98.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 117.36 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.081 / Net I/σ(I): 7.4
Reflection shellResolution: 3.9→4.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Rsym value: 0.497 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.10.2refinement
XDSdata reduction
BUSTERphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.74→14 Å / Cor.coef. Fo:Fc: 0.7206 / Cor.coef. Fo:Fc free: 0.7075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.977
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 863 4.96 %RANDOM
Rwork0.2336 ---
obs0.2347 17414 46.93 %-
Displacement parametersBiso mean: 138.12 Å2
Baniso -1Baniso -2Baniso -3
1--144.6946 Å20 Å2127.9856 Å2
2--36.7782 Å20 Å2
3---107.9164 Å2
Refine analyzeLuzzati coordinate error obs: 0.741 Å
Refinement stepCycle: LAST / Resolution: 3.74→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12359 0 0 5 12364
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112697HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1217410HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4080SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes245HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1853HARMONIC5
X-RAY DIFFRACTIONt_it12697HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion22.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1760SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14580SEMIHARMONIC4
LS refinement shellResolution: 3.74→3.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.4527 46 5.96 %
Rwork0.27 726 -
all0.2796 772 -
obs--12.66 %
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)
13.7720.12134.99430.08321.25237.6446-0.0478-0.2931.1565-0.6224-0.686-0.0311-0.1624-0.18590.73380.42450.2211-0.276-0.39520.24340.054637.5949-7.054830.6532
26.04560.04457.749900.145710.20040.6647-0.35660.0747-0.0787-0.49610.67680.9874-0.3676-0.16860.3732-0.1719-0.2197-0.04980.0522-0.440327.449-29.481735.8057
32.94690.49816.68096.99445.058913.77691.05710.5041-1.2335-1.5072-0.72230.5995-0.03680.7397-0.33481.09490.7676-0.861-0.1185-0.3576-0.397643.164-47.182727.7823
43.6989-8.2239-3.16219.88913.2214.08961.071.7544-0.5912-1.3928-0.7991-0.5378-1.3176-0.3313-0.2710.71020.8539-0.4961.1415-0.5533-1.298563.3492-35.587717.403
53.5795-0.25664.17970.0833-2.263211.3238-0.33981.45361.1916-0.36440.2368-0.2917-0.03831.29160.1030.47140.16580.14631.05640.7856-0.962659.6935-10.835719.1513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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