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- PDB-4zzc: The GLIC pentameric Ligand-Gated Ion Channel open form complexed ... -

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Basic information

Entry
Database: PDB / ID: 4zzc
TitleThe GLIC pentameric Ligand-Gated Ion Channel open form complexed to xenon
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / potassium channel activity / 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 / XENON / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsSauguet, L. / Fourati, Z. / Prange, T. / Delarue, M. / Colloc'h, N.
CitationJournal: Plos One / Year: 2016
Title: Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel.
Authors: Sauguet, L. / Fourati, Z. / Prange, T. / Delarue, M. / Colloc'h, N.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2May 8, 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)195,52572
Polymers181,3895
Non-polymers14,13667
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39900 Å2
ΔGint-213 kcal/mol
Surface area61580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.000, 132.820, 159.150
Angle α, β, γ (deg.)90.00, 101.88, 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 / GLIC pentameric ligand-gated ion channel


Mass: 36277.723 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Strain: PCC 7421 / 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 , 6 types, 68 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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 / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / 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: Chemical...
ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Xe
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.13 Å3/Da / Density % sol: 76.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 12-15% PEG4000 0.1M Na Acetate pH4 0.4M NaSCN 15% glycerol 5% DMSO
PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.182 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.182 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Biso Wilson estimate: 78.85 Å2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementResolution: 3.1→25 Å / Cor.coef. Fo:Fc: 0.9075 / Cor.coef. Fo:Fc free: 0.8982 / SU R Cruickshank DPI: 0.64 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.542 / SU Rfree Blow DPI: 0.299 / SU Rfree Cruickshank DPI: 0.315
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 3362 5.08 %RANDOM
Rwork0.208 ---
obs0.2089 66209 99.66 %-
Displacement parametersBiso mean: 88.07 Å2
Baniso -1Baniso -2Baniso -3
1--11.2538 Å20 Å222.6343 Å2
2---1.2804 Å20 Å2
3---12.5342 Å2
Refine analyzeLuzzati coordinate error obs: 0.634 Å
Refinement stepCycle: LAST / Resolution: 3.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12677 0 383 7 13067
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913475HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0418297HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4644SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes262HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1924HARMONIC5
X-RAY DIFFRACTIONt_it13475HARMONIC20
X-RAY DIFFRACTIONt_nbd18SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion19.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1772SEMIHARMONIC5
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_contact15442SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 270 5.55 %
Rwork0.2384 4599 -
all0.2406 4869 -
obs--99.66 %
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)
11.6896-0.43791.29270.862-0.58032.8440.0041-0.03190.1712-0.05420.04430.0712-0.346-0.3335-0.04850.05430.0928-0.1364-0.18260.0519-0.19839.9925-6.507429.8128
22.42190.21132.30480.75920.42363.58360.1224-0.0038-0.09010.0337-0.00450.24780.0311-0.2993-0.1179-0.17640.0383-0.0972-0.00490.0137-0.151327.9957-27.794435.9225
31.30670.36881.29610.82230.91153.52860.15550.0322-0.2793-0.074-0.08370.16270.303-0.158-0.07180.00910.0047-0.2222-0.1908-0.0617-0.096241.943-47.518928.8846
41.12490.07711.1030.80570.39154.55830.03820.2857-0.2102-0.2463-0.016-0.122-0.04220.3065-0.02220.00960.1069-0.1301-0.1446-0.1186-0.211162.7923-38.375617.8835
51.3853-0.43751.57570.8865-0.82254.47550.01280.13970.1655-0.2633-0.0474-0.143-0.09110.0820.03470.0473-0.0442-0.0562-0.16690.0486-0.21961.5929-13.110918.5735
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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