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- PDB-6i08: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT E243C-I201W -

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Basic information

Entry
Database: PDB / ID: 6i08
TitleTHE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT E243C-I201W
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
DIUNDECYL PHOSPHATIDYL CHOLINE / 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 25, 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
D: Proton-gated ion channel
A: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
E: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,50723
Polymers181,5445
Non-polymers3,96318
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28310 Å2
ΔGint-302 kcal/mol
Surface area62820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.800, 134.350, 159.350
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 6 molecules DABCE

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36308.738 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
#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

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Non-polymers , 4 types, 88 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 71 / 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: 191 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationMonochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3→48.9 Å / Num. obs: 73894 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 79.75 Å2 / Net I/σ(I): 12.5
Reflection shellResolution: 3→3.06 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTER2.10.3refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.856 / SU R Cruickshank DPI: 0.482 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.43 / SU Rfree Blow DPI: 0.273 / SU Rfree Cruickshank DPI: 0.287
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3674 4.99 %RANDOM
Rwork0.209 ---
obs0.21 73659 99 %-
Displacement parametersBiso mean: 102.4 Å2
Baniso -1Baniso -2Baniso -3
1--24.7431 Å20 Å254.9739 Å2
2---0.335 Å20 Å2
3---25.0782 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12640 0 209 71 12920
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113181HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1217995HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4439SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes255HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1885HARMONIC5
X-RAY DIFFRACTIONt_it13181HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion20.83
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_contact15190SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2787 282 5.15 %
Rwork0.2609 5190 -
all0.2619 5472 -
obs--99.67 %

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