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- PDB-5mzq: X-ray structure of the M205W mutant of GLIC in complex with bromoform -

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Basic information

Entry
Database: PDB / ID: 5mzq
TitleX-ray structure of the M205W mutant of GLIC in complex with bromoform
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium 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
(3R)-3-(dodecanoyloxy)tetradecanoic acid / ACETATE ION / DODECANE / TRIBROMOMETHANE / 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFourati, Z. / Delarue, M.
CitationJournal: Cell Rep / Year: 2018
Title: Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels.
Authors: Fourati, Z. / Howard, R.J. / Heusser, S.A. / Hu, H. / Ruza, R.R. / Sauguet, L. / Lindahl, E. / Delarue, M.
History
DepositionFeb 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell

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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)196,17054
Polymers187,3705
Non-polymers8,80049
Water7,206400
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38150 Å2
ΔGint-224 kcal/mol
Surface area62200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.969, 131.779, 160.404
Angle α, β, γ (deg.)90.00, 102.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-570-

HOH

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Components

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Protein , 1 types, 5 molecules ABCDE

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


Mass: 37473.910 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

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Non-polymers , 8 types, 449 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-PC8 / 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 510.622 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H49NO8P
#4: Chemical
ChemComp-2IL / (3R)-3-(dodecanoyloxy)tetradecanoic acid


Mass: 426.673 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C26H50O4
#5: Chemical
ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C12H26
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-MBR / TRIBROMOMETHANE / Bromoform


Mass: 252.731 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CHBr3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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 Å3/Da
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM NaAct pH4 400 mM NaSCN 16% glycerol 2% DMSO 12-15 % PEG4K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 89066 / % possible obs: 97 % / Redundancy: 5.1 % / Biso Wilson estimate: 63.24 Å2 / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.84 Å / Cor.coef. Fo:Fc: 0.9143 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.335 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 4467 5.02 %RANDOM
Rwork0.2016 ---
obs0.2025 89066 98.35 %-
Displacement parametersBiso mean: 66.01 Å2
Baniso -1Baniso -2Baniso -3
1--4.6247 Å20 Å212.6546 Å2
2---0.4025 Å20 Å2
3---5.0273 Å2
Refine analyzeLuzzati coordinate error obs: 0.419 Å
Refinement stepCycle: 1 / Resolution: 2.8→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12708 0 495 400 13603
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913505HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0218338HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4629SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes265HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1912HARMONIC5
X-RAY DIFFRACTIONt_it13505HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion19.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1771SEMIHARMONIC5
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_contact15557SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2707 327 4.94 %
Rwork0.2632 6290 -
all0.2636 6617 -
obs--98.94 %
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)
10.492-0.26810.66140.4368-0.35511.61360.0371-0.04530.0788-0.0008-0.00180.0673-0.0872-0.0213-0.03530.10650.0625-0.147-0.02950.0061-0.099340.1357-6.361730.4994
21.13010.09291.41650.23370.24352.41620.015-0.0114-0.03830.0855-0.02230.1277-0.0043-0.02710.0074-0.00930.0105-0.13450.08660.0171-0.0727.989-27.728236.2198
30.63630.15060.72180.47130.27771.75040.0246-0.0385-0.1287-0.0112-0.06130.08580.0380.03330.03670.0540.0464-0.1936-0.0383-0.0329-0.04142.4309-47.272729.2368
40.51110.03230.7940.35940.15272.3340.0147-0.0247-0.0623-0.1123-0.0354-0.1345-0.02460.0350.02070.05810.0545-0.13720.0063-0.0631-0.070963.4069-37.838418.5193
50.4619-0.20430.72180.4588-0.48092.1390.0057-0.05940.0933-0.12080.0078-0.0893-0.05550.037-0.01350.1188-0.0444-0.1442-0.04280.0146-0.104962.033-12.560519.59
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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