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- PDB-6hya: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Q193L -

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Basic information

Entry
Database: PDB / ID: 6hya
TitleTHE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Q193L
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: 3.39 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 19, 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

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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)182,07211
Polymers181,3845
Non-polymers6886
Water181
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22640 Å2
ΔGint-187 kcal/mol
Surface area62420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.240, 133.320, 157.720
Angle α, β, γ (deg.)90.00, 100.96, 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: 36276.777 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: 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
#4: 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: 0.9789 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: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.39→48.84 Å / Num. obs: 50723 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 106.02 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 4.9
Reflection shellResolution: 3.39→3.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.4 / % possible all: 92.6

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTER2.10.2refinement
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.39→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.9011 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.606
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1268 4.98 %RANDOM
Rwork0.1838 ---
obs0.1852 25470 49.98 %-
Displacement parametersBiso mean: 110.86 Å2
Baniso -1Baniso -2Baniso -3
1--30.3103 Å20 Å228.8528 Å2
2--21.065 Å20 Å2
3---9.2454 Å2
Refine analyzeLuzzati coordinate error obs: 0.448 Å
Refinement stepCycle: LAST / Resolution: 3.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12620 0 17 1 12638
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112971HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1217730HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4299SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes255HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it12971HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion21.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1760SEMIHARMONIC5
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_contact15086SEMIHARMONIC4
LS refinement shellResolution: 3.39→3.53 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3149 37 5.2 %
Rwork0.2343 674 -
all0.239 711 -
obs--12.44 %
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)
12.4228-0.49032.12921.1845-0.87484.2774-0.11730.06790.3712-0.4180.02340.2317-0.4151-0.25390.0939-0.19210.13720.0137-0.11790.0744-0.045339.2906-5.322330.2316
23.7328-0.2034.15770.67030.03525.90510.1657-0.1143-0.0577-0.2925-0.02690.43450.0527-0.3931-0.1389-0.4471-0.05330.09960.20650.08640.052329.0896-27.801635.5725
32.27580.69953.18541.10561.20176.31750.0465-0.066-0.1741-0.38480.03460.37560.2346-0.2118-0.0811-0.2156-0.0262-0.0497-0.1635-0.00540.013244.2083-46.134227.4846
41.09570.33471.29191.30040.87615.2992-0.03860.3839-0.2641-0.55870.11140.0819-0.0160.555-0.0728-0.30230.05620.15120.1717-0.1747-0.156564.2037-34.947416.6781
51.9048-0.47992.80810.875-1.67587.4581-0.16580.37710.1575-0.46420.1050.004-0.19750.39550.0608-0.1166-0.22130.1080.01380.131-0.182460.9936-9.708718.4387
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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