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- PDB-6f0r: GLIC mutant E82Q -

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Basic information

Entry
Database: PDB / ID: 6f0r
TitleGLIC mutant E82Q
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / potassium 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 / 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
ACETATE ION / DIUNDECYL PHOSPHATIDYL CHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsHu, H.D. / Delarue, M.
CitationJournal: PLoS Biol. / Year: 2017
Title: Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel.
Authors: Nemecz, A. / Hu, H. / Fourati, Z. / Van Renterghem, C. / Delarue, M. / Corringer, P.J.
History
DepositionNov 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,31731
Polymers181,3845
Non-polymers6,93326
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32020 Å2
ΔGint-157 kcal/mol
Surface area62090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.840, 132.420, 160.060
Angle α, β, γ (deg.)90.00, 102.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 11 molecules ABCDE

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


Mass: 36276.738 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#5: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 56 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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

Crystal growTemperature: 293 K / Method: evaporation
Details: 12% PEG4K, 15% glycerol, 100 mM Acetate de Sodium pH4, 400 mM Sodium isothiocyanate, 3% DMSO

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.5→49 Å / Num. obs: 112433 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 57.79 Å2 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.64 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.849 / SU R Cruickshank DPI: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4724 4.97 %RANDOM
Rwork0.241 ---
obs0.241 95038 74.7 %-
Displacement parametersBiso mean: 70.73 Å2
Baniso -1Baniso -2Baniso -3
1--7.6678 Å20 Å2-2.4986 Å2
2--21.6505 Å20 Å2
3----13.9827 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: 1 / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12625 0 287 36 12948
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113261HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1418070HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4509SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1900HARMONIC5
X-RAY DIFFRACTIONt_it13261HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion18.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1770SEMIHARMONIC5
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_contact14786SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3639 -5.26 %
Rwork0.3191 1530 -
all0.3215 1615 -
obs--17.2 %
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)
12.353-0.21210.19010.5765-0.33563.12360.24521.13270.41750.05990.0520.0683-0.5134-1.126-0.2972-0.40750.39670.07110.69480.3215-0.519840.2669-6.619930.1911
22.66270.09361.05440.6916-0.09023.71430.12841.0232-0.04340.0489-0.02420.143-0.0352-0.9646-0.1042-0.58690.1875-0.00060.8944-0.0375-0.618127.8324-27.73736.2977
32.4730.08240.64740.6490.49413.6390.02781.3049-0.55210.0644-0.09120.02910.2909-0.80370.0634-0.5575-0.0677-0.00370.7374-0.3749-0.461441.9981-47.476529.2143
42.18540.1847-0.30050.52220.22823.3687-0.09411.3253-0.3462-0.0615-0.0368-0.11020.0142-0.54480.1309-0.5270.0593-0.0370.6192-0.2986-0.480563.0971-38.531318.3916
51.7787-0.33640.42920.6605-0.44423.39040.26511.14330.27-0.0739-0.1516-0.1605-0.3954-0.415-0.1135-0.43670.26980.03830.60210.198-0.525861.9441-13.242619.068
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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