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- PDB-6fli: The active form of a pentameric ion channel (sTeLIC) gated by alk... -

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Basic information

Entry
Database: PDB / ID: 6fli
TitleThe active form of a pentameric ion channel (sTeLIC) gated by alkaline pH - Co-crystallization with 4-bromo cinnamic acid
ComponentsCys-loop ligand-gated ion channel
KeywordsMEMBRANE PROTEIN / Pentameric ligand-gated ion channel.
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / membrane / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
3-(4-bromophenyl)propanoic acid / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesendosymbiont of Tevnia jerichonana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsHu, H. / Delarue, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation.
Authors: Hu, H. / Nemecz, A. / Van Renterghem, C. / Fourati, Z. / Sauguet, L. / Corringer, P.J. / Delarue, M.
History
DepositionJan 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,23115
Polymers186,5545
Non-polymers2,67710
Water1,910106
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27070 Å2
ΔGint-44 kcal/mol
Surface area61050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.690, 112.660, 144.830
Angle α, β, γ (deg.)90.00, 111.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cys-loop ligand-gated ion channel


Mass: 37310.820 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) endosymbiont of Tevnia jerichonana (bacteria)
Gene: TevJSym_bc00020 / Production host: Escherichia coli (E. coli) / References: UniProt: G2FID1
#2: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-DQZ / 3-(4-bromophenyl)propanoic acid


Mass: 229.071 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H9BrO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 4.54 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 291 K / Method: evaporation / Details: 150mM MgCl2 100mM Tris 8.0 35% PEG 200

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 3→49.32 Å / Num. obs: 66506 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.08 Å2 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.07 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.386
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2255 4.86 %RANDOM
Rwork0.198 ---
obs0.2 46370 69.4 %-
Displacement parametersBiso mean: 50.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.0188 Å20 Å22.0068 Å2
2--2.0296 Å20 Å2
3---0.9892 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12810 0 165 106 13081
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113375HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1418160HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4560SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes295HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2005HARMONIC5
X-RAY DIFFRACTIONt_it13375HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion18.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1705SEMIHARMONIC5
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_contact15337SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3365 -4.69 %
Rwork0.2275 1138 -
all0.2321 1194 -
obs--24.26 %
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)
13.7467-0.0274-2.99330.42980.22672.9130.54940.4620.8360.1235-0.00940.2373-0.5847-0.4577-0.54-0.11210.23080.2173-0.22470.15270.1016-51.227719.153529.7589
24.18380.1815-2.93940.7221-0.18092.86080.2607-0.80140.32980.3535-0.02280.1825-0.24720.5163-0.2378-0.1635-0.07960.0767-0.2109-0.147-0.271-38.64829.525648.0501
34.34090.2688-2.69090.5993-0.12972.1081-0.4172-0.628-0.69790.2607-0.02820.13320.41420.3530.4455-0.10930.0580.1167-0.19770.153-0.2159-40.0365-14.620746.1349
44.85150.026-2.99330.49490.03692.6885-0.50410.9014-0.73760.0964-0.04510.30780.5359-0.86320.5491-0.1162-0.24150.167-0.0615-0.2170.1529-53.3969-19.899226.6187
54.0848-0.2219-2.89170.58160.1322.70280.15561.23310.1645-0.003-0.07060.3428-0.1885-1.1991-0.085-0.35780.069-0.10870.54690.0014-0.1194-60.32531.032816.4539
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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