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- PDB-6f15: GLIC mutant H127Q -

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Basic information

Entry
Database: PDB / ID: 6f15
TitleGLIC mutant H127Q
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: 2.85 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 21, 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)191,52744
Polymers181,2585
Non-polymers10,26939
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36730 Å2
ΔGint-262 kcal/mol
Surface area61910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.210, 133.100, 161.770
Angle α, β, γ (deg.)90.00, 102.82, 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: 36251.641 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Strain: PCC 7421 / 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, 105 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.: 10 / 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.: 72 / 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: 5.4 Å3/Da / Density % sol: 77.22 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 100 mM NaAcetate pH 4 400mM NaSCN 12-15% PEG4000 165% glycerol 3%DMSO

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.85→49.86 Å / Num. obs: 88185 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 66.8 Å2 / Net I/σ(I): 9.8
Reflection shellResolution: 2.85→2.9 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.85→25 Å / Cor.coef. Fo:Fc: 0.8939 / Cor.coef. Fo:Fc free: 0.8717 / SU R Cruickshank DPI: 0.486 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.432 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.294
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 3626 4.95 %RANDOM
Rwork0.2012 ---
obs0.2026 73315 83.06 %-
Displacement parametersBiso mean: 59.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.0834 Å20 Å2-6.2284 Å2
2--10.3436 Å20 Å2
3----10.2601 Å2
Refine analyzeLuzzati coordinate error obs: 0.386 Å
Refinement stepCycle: 1 / Resolution: 2.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12675 0 415 72 13162
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113391HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0918205HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4624SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes270HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1905HARMONIC5
X-RAY DIFFRACTIONt_it13391HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion18.81
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_contact14529SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3217 81 4.04 %
Rwork0.2597 1926 -
all0.2624 2007 -
obs--30.99 %
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)
11.7316-0.2860.52790.7099-0.32872.38790.14580.63680.2586-0.00460.01930.0827-0.369-0.6985-0.1651-0.15750.2647-0.02810.21210.2066-0.368240.6688-6.61530.6967
22.26430.15360.9840.42150.1052.51690.08360.7548-0.02380.0948-0.03970.1198-0.0306-0.6014-0.0439-0.31930.1503-0.08070.4508-0.0169-0.364128.4353-27.974536.5771
31.8720.07080.81720.65410.23832.70960.04090.8272-0.3954-0.0024-0.07290.05470.2763-0.41290.032-0.3006-0.0371-0.10460.2693-0.2395-0.291342.6784-47.659829.5275
41.53380.09270.06350.59420.32332.994-0.04740.8303-0.2538-0.103-0.0221-0.1195-0.0721-0.36460.0695-0.26980.0514-0.0940.1779-0.2235-0.313763.7726-38.456718.8068
51.2825-0.19270.55460.6878-0.42723.58430.15010.71070.2638-0.1226-0.098-0.1607-0.2149-0.3847-0.0521-0.17010.1773-0.01710.21880.1326-0.351262.4616-13.117519.6011
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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