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- PDB-5muo: X-ray structure of the 2-22' locally-closed mutant of GLIC in com... -

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Basic information

Entry
Database: PDB / ID: 5muo
TitleX-ray structure of the 2-22' locally-closed 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 / 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 / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsFourati, Z. / Ruza, R.R. / 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 13, 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 1.2Jan 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)183,73216
Polymers182,6305
Non-polymers1,10211
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24610 Å2
ΔGint-193 kcal/mol
Surface area63930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.980, 132.900, 159.920
Angle α, β, γ (deg.)90.00, 101.84, 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 ABCDE

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


Mass: 36525.922 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 (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: 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, 86 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PFL / 2,6-BIS(1-METHYLETHYL)PHENOL / 2,6-DIISOPROPYLPHENOL / PROPOFOL


Mass: 178.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.94 Å3/Da / Density % sol: 75.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PH 4, VAPOR DIFFUSION, TEMPERATURE 293K / PH range: 4

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 3, 2016
RadiationMonochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.9→49.23 Å / Num. obs: 78570 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 98.23 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.042 / Net I/σ(I): 13
Reflection shellResolution: 2.9→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2 / Rsym value: 0.395 / % possible all: 96.5

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTER2.10.2refinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TLV

3tlv


Resolution: 3.19→20 Å / Cor.coef. Fo:Fc: 0.9278 / Cor.coef. Fo:Fc free: 0.9222 / SU R Cruickshank DPI: 0.715 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.595 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.302
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 3069 5.09 %RANDOM
Rwork0.1892 ---
obs0.19 60276 97.9 %-
Displacement parametersBiso mean: 102.19 Å2
Baniso -1Baniso -2Baniso -3
1--3.936 Å20 Å220.7306 Å2
2---2.067 Å20 Å2
3---6.003 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 3.19→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12648 0 46 76 12770
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113038HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1217836HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4313SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes263HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1899HARMONIC5
X-RAY DIFFRACTIONt_it13038HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion18.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1769SEMIHARMONIC5
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_contact15116SEMIHARMONIC4
LS refinement shellResolution: 3.19→3.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3208 210 5.12 %
Rwork0.2602 3895 -
all0.2633 4105 -
obs--90.06 %
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)
11.62130.05671.78590.3176-0.29053.12630.0233-0.04260.1548-0.04390.05410.1017-0.1826-0.0392-0.07740.1190.1205-0.2269-0.0923-0.0192-0.128939.3868-5.928930.1517
21.97790.01822.31960.36680.25013.23880.0523-0.0461-0.05260.0546-0.00040.1657-0.0755-0.1242-0.0519-0.1149-0.0006-0.14090.17940.0465-0.16628.2597-27.632735.6829
31.19930.16441.97220.60670.36513.57670.0644-0.04-0.1705-0.0469-0.01110.09880.09160.02-0.05330.07330.0545-0.3047-0.1214-0.0468-0.050942.9115-46.327628.1661
40.66910.07481.4180.5158-0.01493.62880.05140.0549-0.2169-0.1459-0.0518-0.1317-0.0370.11560.00040.01940.2061-0.17930.0725-0.1553-0.194963.4259-36.197917.4964
50.6892-0.23981.25820.674-0.69683.4373-0.03070.02820.0761-0.15390.0969-0.0615-0.03150.1261-0.06630.0636-0.1035-0.18080.02210.0481-0.215761.0926-11.257618.7443
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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