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- PDB-5mvn: X-ray structure of the M205W mutant of GLIC in complex with propofol -

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Basic information

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


sodium channel activity / potassium channel activity / transmembrane transporter complex / 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 / 2,6-BIS(1-METHYLETHYL)PHENOL / DIUNDECYL PHOSPHATIDYL CHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 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
DepositionJan 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 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
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)195,76053
Polymers181,6645
Non-polymers14,09648
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41460 Å2
ΔGint-233 kcal/mol
Surface area61270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.229, 132.474, 159.759
Angle α, β, γ (deg.)90.00, 102.50, 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: 36332.734 Da / Num. of mol.: 5
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
#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, 70 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: Chemical
ChemComp-PFL / 2,6-BIS(1-METHYLETHYL)PHENOL / 2,6-DIISOPROPYLPHENOL / PROPOFOL


Mass: 178.271 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 5.15 Å3/Da / Density % sol: 76.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 400 mM NaSCN 100 mM NaAcetate pH4 12-15 % PEG4K 16 % glycerol 2 % DMSO

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97 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: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 33576 / % possible obs: 98 % / Redundancy: 2.5 % / Biso Wilson estimate: 72.57 Å2 / Net I/σ(I): 3.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HFI

4hfi


Resolution: 3.49→49.28 Å / Cor.coef. Fo:Fc: 0.8117 / Cor.coef. Fo:Fc free: 0.8213 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.411
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 2365 5.07 %RANDOM
Rwork0.2176 ---
obs0.2183 46605 99.12 %-
Displacement parametersBiso mean: 92.08 Å2
Baniso -1Baniso -2Baniso -3
1--14.4868 Å20 Å232.9425 Å2
2---3.2691 Å20 Å2
3---17.756 Å2
Refine analyzeLuzzati coordinate error obs: 0.486 Å
Refinement stepCycle: 1 / Resolution: 3.49→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12655 0 527 28 13210
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913483HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9718307HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4607SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1936HARMONIC5
X-RAY DIFFRACTIONt_it13483HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion19.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1765SEMIHARMONIC5
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_contact15322SEMIHARMONIC4
LS refinement shellResolution: 3.49→3.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2926 148 4.52 %
Rwork0.252 3126 -
all0.2537 3274 -
obs--94.68 %
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)
10.6613-0.04380.91940.1795-0.19171.56360.0365-0.04660.08550.00020.03660.038-0.1236-0.025-0.07310.12320.1208-0.1055-0.02390.0014-0.098740.057-6.469130.5569
20.90840.00481.446800.29092.77150.0277-0.0051-0.07310.12920.00290.1332-0.0526-0.018-0.0306-0.0722-0.0111-0.070.08050.0478-0.023728.1444-27.990636.4353
30.44130.17120.94090.36630.20231.90690.0533-0.0476-0.1868-0.0397-0.05150.0946-0.01290.0377-0.00180.03440.0702-0.1865-0.0667-0.05350.051342.5671-47.446329.2077
40.42010.1080.84810.13990.11592.21630.0308-0.0451-0.1023-0.1259-0.0393-0.1104-0.05120.05240.00850.01130.1235-0.05460.0329-0.1066-0.055363.4991-37.963118.4246
50.5442-0.18540.97870.1911-0.25552.34970.0313-0.07720.053-0.13610.016-0.0786-0.08430.0368-0.04730.1198-0.0915-0.0493-0.01750.0289-0.098361.9172-12.601819.3079
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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