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- PDB-6hyx: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Y197F-P250C -

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Basic information

Entry
Database: PDB / ID: 6hyx
TitleTHE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Y197F-P250C
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / PENTAMERIC TRANSMEMBRANE CHANNEL / ION CHANNEL.
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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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)182,10718
Polymers181,2585
Non-polymers84913
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23380 Å2
ΔGint-272 kcal/mol
Surface area63470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.810, 134.230, 160.300
Angle α, β, γ (deg.)90.00, 102.09, 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: 36251.684 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 (bacteria)
Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.99 Å3/Da / Density % sol: 75.36 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4
Details: PH 4, VAPOR DIFFUSION, TEMPERATURE 293K.12-14.5% PEG4K; 15% GLycerol; 400 mM NaSCN; 3% DMSO; 100mM NaAcetate pH 4
PH range: 4

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2015
RadiationMonochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→49.37 Å / Num. obs: 75432 / % possible obs: 99.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 80.96 Å2 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.06 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.5 / % possible all: 99

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTER2.10.3refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 1.092 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.809 / SU Rfree Blow DPI: 0.336 / SU Rfree Cruickshank DPI: 0.354
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2831 5.09 %RANDOM
Rwork0.209 ---
obs0.209 55640 73.6 %-
Displacement parametersBiso mean: 70.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.2643 Å20 Å2-4.6654 Å2
2--4.7275 Å20 Å2
3----4.4633 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12585 0 24 1 12610
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112956HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0717710HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4319SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1875HARMONIC5
X-RAY DIFFRACTIONt_it12956HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion18.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1765SEMIHARMONIC5
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_contact14752SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3285 -5.55 %
Rwork0.2789 1498 -
all0.2817 1586 -
obs--28.42 %
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)
12.3740.01292.14020.4698-0.46384.3516-0.1544-0.02360.3076-0.12390.12590.1287-0.6004-0.22720.02840.24260.2183-0.1189-0.1551-0.0393-0.100839.6859-4.959530.113
23.30050.32773.50180.65790.60414.49840.1816-0.3759-0.21660.1157-0.01510.1895-0.0627-0.7494-0.1665-0.293-0.05530.03640.38290.1326-0.124828.6539-26.840235.8659
32.00560.41152.29790.71660.79125.28730.2983-0.0536-0.5227-0.0183-0.00640.16630.4777-0.1288-0.29190.17810.0642-0.3964-0.3208-0.05280.205243.2572-45.777128.4408
40.94720.43851.59581.15250.3944.92190.1520.2588-0.3524-0.35690.1003-0.20880.09280.4362-0.2522-0.11530.3432-0.01960.2355-0.3231-0.091163.8568-35.894417.7096
51.3778-0.50822.00481.0895-0.91285.657-0.07110.2990.1335-0.29760.0771-0.1597-0.20040.4841-0.0060.0693-0.25790.0180.03560.0866-0.173761.6875-10.58218.7676
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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