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- PDB-6hyw: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Y119F -

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Basic information

Entry
Database: PDB / ID: 6hyw
TitleTHE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Y119F
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / PENTAMERIC TRANSMEMBRANE CHANNEL / ION CHANNEL.
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
ACETATE ION / DIUNDECYL PHOSPHATIDYL CHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsHu, H.D. / Delarue, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel.
Authors: Hu, H. / Ataka, K. / Menny, A. / Fourati, Z. / Sauguet, L. / Corringer, P.J. / Koehl, P. / Heberle, J. / Delarue, M.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 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)191,57744
Polymers181,3095
Non-polymers10,26939
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37050 Å2
ΔGint-254 kcal/mol
Surface area60600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.000, 132.240, 161.480
Angle α, β, γ (deg.)90.00, 103.25, 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: 36261.723 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus PCC 7421 (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, 204 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.: 171 / 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: 291 K / Method: evaporation
Details: 12-14.5% PEG4K; 15% GLycerol; 400 mM NaSCN; 3% DMSO; 100mM NaAcetate pH 4.

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9771 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionResolution: 2.8→48.34 Å / Num. obs: 85783 / % possible obs: 93.2 % / Redundancy: 2.3 % / Biso Wilson estimate: 59.02 Å2 / Net I/σ(I): 9.9
Reflection shellResolution: 2.8→2.85 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.447 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.279
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3573 5.02 %RANDOM
Rwork0.192 ---
obs0.193 71170 77.4 %-
Displacement parametersBiso mean: 46.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.9428 Å20 Å2-6.5228 Å2
2--4.3659 Å20 Å2
3----6.3087 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12620 0 415 171 13206
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113396HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0718210HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4619SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes265HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1910HARMONIC5
X-RAY DIFFRACTIONt_it13396HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion18.12
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_contact15134SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2526 102 4.95 %
Rwork0.2363 1959 -
all0.2372 2061 -
obs--30.34 %
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)
10.6088-0.17520.32270.5376-0.19491.14960.0501-0.08680.1514-0.0120.02180.0355-0.2001-0.1371-0.07190.04370.0627-0.0932-0.03220.0019-0.14840.4601-6.786830.3611
21.70820.11711.48590.38290.20912.08880.0183-0.0579-0.04840.1142-0.01930.1848-0.0058-0.10350.001-0.12520.0219-0.06960.0967-0.0025-0.130428.2718-27.871936.2054
30.91720.19070.8120.55880.47621.83050.0204-0.0206-0.24360.0011-0.04550.0820.105-0.01640.0251-0.03910.0221-0.1311-0.044-0.005-0.076842.3297-47.432929.2293
40.670.03870.48850.41890.47142.45620.0210.0278-0.1638-0.1261-0.0049-0.1706-0.02030.1392-0.0161-0.02850.0416-0.0943-0.0463-0.0445-0.100663.2998-38.337518.7289
50.5584-0.0880.41310.5007-0.39761.64560.0137-0.02330.1381-0.125-0.0049-0.2023-0.08380.0824-0.00880.0317-0.0212-0.0705-0.04850.0115-0.12462.0904-13.222119.4698
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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