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- PDB-6hz1: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT E243C -

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Basic information

Entry
Database: PDB / ID: 6hz1
TitleTHE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT E243C
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
ACETATE ION / DIUNDECYL PHOSPHATIDYL CHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 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 / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
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)194,63149
Polymers181,2495
Non-polymers13,38344
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38410 Å2
ΔGint-253 kcal/mol
Surface area62130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.900, 132.950, 160.060
Angle α, β, γ (deg.)90.00, 102.41, 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: 36249.711 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / 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, 268 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.: 15 / 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.: 230 / 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: 5.18 Å3/Da / Density % sol: 76.25 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 4
Details: 12-15% PEG4K, 0.1M NA ACETATE PH4, 0.4M NASCN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
PH range: 4

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.5→49.07 Å / Num. obs: 122120 / % possible obs: 95.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 41.88 Å2 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.5 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementResolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.887 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.216
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4903 4.98 %RANDOM
Rwork0.205 ---
obs0.206 98530 77.3 %-
Displacement parametersBiso mean: 49.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.4229 Å20 Å2-4.2048 Å2
2--3.8133 Å20 Å2
3----2.3904 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12610 0 475 230 13315
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813432HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0318224HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4648SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1904HARMONIC5
X-RAY DIFFRACTIONt_it13432HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion18.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1774SEMIHARMONIC5
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_contact14998SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2209 175 5.28 %
Rwork0.2064 3140 -
all0.2071 3315 -
obs--35.31 %
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)
10.9249-0.07720.7780.3524-0.29291.3520.05440.01960.15870.02440.00680.0704-0.2018-0.0807-0.06120.080.1565-0.1375-0.0895-0.0171-0.04739.9191-6.831530.669
21.69130.09561.85780.36460.10272.20840.03610.0183-0.02150.0663-0.01220.1804-0.0421-0.0932-0.0239-0.14280.061-0.10190.1483-0.0434-0.081128.2183-28.264936.4483
30.6690.11510.84190.56240.43631.92490.0295-0.0041-0.2361-0.0407-0.04990.12890.0699-0.00090.02050.0040.025-0.1596-0.0905-0.0748-0.027442.6017-47.584629.2178
40.25940.13970.2270.37940.32691.92660.03470.0436-0.1518-0.1487-0.0509-0.1435-0.04080.05160.01610.04910.1376-0.08590.0166-0.0764-0.110463.3638-37.881718.5525
50.2808-0.13180.54960.4115-0.48552.40930.0373-0.00260.1318-0.1433-0.0061-0.1515-0.11290.0646-0.03120.0931-0.0181-0.0849-0.05060.0694-0.102961.6966-12.70419.6158
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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