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- PDB-6f0n: GLIC mutant E82A -

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Basic information

Entry
Database: PDB / ID: 6f0n
TitleGLIC mutant E82A
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / 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 / 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: 3.2 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 / 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

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)188,25339
Polymers181,0985
Non-polymers7,15434
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33150 Å2
ΔGint-239 kcal/mol
Surface area61300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.220, 132.600, 159.030
Angle α, β, γ (deg.)90.00, 101.65, 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: 36219.688 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
#6: 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, 130 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 5.14 Å3/Da / Density % sol: 76.06 %
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: 0.9194 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 3.2→49.31 Å / Num. obs: 60439 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 85.95 Å2 / Net I/σ(I): 8.5
Reflection shellResolution: 3.2→3.28 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 3.2→25 Å / Cor.coef. Fo:Fc: 0.8932 / Cor.coef. Fo:Fc free: 0.8591 / SU R Cruickshank DPI: 0.851 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.7 / SU Rfree Blow DPI: 0.33 / SU Rfree Cruickshank DPI: 0.346
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 3053 5.06 %RANDOM
Rwork0.2095 ---
obs0.2106 60319 99.87 %-
Displacement parametersBiso mean: 78.04 Å2
Baniso -1Baniso -2Baniso -3
1--10.1438 Å20 Å220.301 Å2
2--1.2242 Å20 Å2
3---8.9195 Å2
Refine analyzeLuzzati coordinate error obs: 0.451 Å
Refinement stepCycle: 1 / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12660 0 295 102 13057
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913271HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0118095HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4514SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1910HARMONIC5
X-RAY DIFFRACTIONt_it13271HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion17.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1775SEMIHARMONIC5
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_contact15054SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 212 4.77 %
Rwork0.2483 4234 -
all0.2486 4446 -
obs--99.87 %
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)
11.0324-0.05681.06960.5237-0.32952.06260.021-0.06460.03190.01770.09570.0349-0.1933-0.1226-0.11670.10140.0909-0.1378-0.1043-0.0104-0.116540.3624-6.732130.0595
22.14170.22882.70830.70190.26154.17170.0834-0.056-0.09540.08280.02170.1870.0386-0.1257-0.1052-0.04170.0343-0.08880.01510.0167-0.114428.2058-27.852236.0945
30.83340.31021.00910.47810.50632.66740.0283-0.0073-0.1825-0.0028-0.01520.11930.1375-0.0161-0.01310.08510.065-0.2212-0.1296-0.0291-0.004342.213-47.484729.0339
40.75290.06321.13310.47820.42093.98290.02710.0953-0.132-0.1370.0199-0.0924-0.11230.1744-0.0470.05950.0414-0.1512-0.0777-0.0353-0.078563.0593-38.457917.9821
51.0259-0.43051.31260.5623-0.93593.81050.02010.05030.1044-0.0917-0.0128-0.1463-0.02410.06-0.00730.0983-0.0269-0.1185-0.1156-0.0042-0.083961.825-13.211718.6782
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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