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- PDB-6fl9: The active form of a pentameric ion channel (sTeLIC) gated by alk... -

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Basic information

Entry
Database: PDB / ID: 6fl9
TitleThe active form of a pentameric ion channel (sTeLIC) gated by alkaline pH - Wild type 2.3 Angstrom resolution
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 / transmembrane signaling receptor activity / membrane
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
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesendosymbiont of Tevnia jerichonana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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 25, 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

Downloads & links

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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)189,05715
Polymers186,5545
Non-polymers2,50310
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29920 Å2
ΔGint-30 kcal/mol
Surface area61660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.600, 112.960, 144.430
Angle α, β, γ (deg.)90.00, 112.05, 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: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 4.45 Å3/Da / Density % sol: 72.36 %
Crystal growTemperature: 290 K / Method: evaporation
Details: 100 mM Tris pH 8.0; 150 mM MgCl2; 3% DMSO; 32% PEG 200

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→49.34 Å / Num. obs: 144663 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.46 Å2 / Net I/σ(I): 6.4
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.883 / SU R Cruickshank DPI: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.236 6386 4.92 %RANDOM
Rwork0.209 ---
obs0.21 129879 89.7 %-
Displacement parametersBiso mean: 80.66 Å2
Baniso -1Baniso -2Baniso -3
1-6.49 Å20 Å27.9959 Å2
2---5.6045 Å20 Å2
3----0.8855 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: 1 / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12830 0 170 403 13403
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113360HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0818100HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4605SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes300HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1915HARMONIC5
X-RAY DIFFRACTIONt_it13360HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion18.53
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_contact14999SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1984 397 5.07 %
Rwork0.1828 7430 -
all0.1836 7827 -
obs--73.3 %
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)
16.5717-1.668-4.43443.51861.16984.35080.54730.63830.8663-0.0273-0.12290.3175-0.5408-0.7245-0.42440.27210.26580.6749-0.23290.12760.1896-66.791720.733941.8625
25.4632-0.5716-3.59983.35530.53023.43660.37860.43450.4146-0.02310.0466-0.1165-0.434-0.4614-0.42520.23780.12470.5947-0.29620.120.1428-26.750517.275310.266
36.8804-0.6177-4.381.94120.69754.31410.1707-1.07260.33460.4820.06990.3623-0.20350.5152-0.24060.2952-0.05790.7102-0.2542-0.12690.0451-54.05948.611160.5733
45.75410.5121-3.65352.97870.25762.83740.2675-0.69680.23590.24280.00650.1-0.31980.5484-0.2740.1739-0.08470.5291-0.2165-0.11770.0763-14.478810.956228.3405
54.66020.7976-3.64522.6499-0.19044.0078-0.3883-0.7231-0.56940.5364-0.13480.2630.53150.30720.52310.3022-0.01430.7225-0.29660.13780.1216-56.7268-16.747756.7718
65.49040.5996-4.1821.91510.03294.0315-0.2234-0.7692-0.48120.2137-0.19320.06840.31120.44230.41660.15260.09030.4802-0.23730.1260.0459-14.1061-11.844828.9297
77.10261.2281-4.33983.0524-0.75373.7614-0.38310.7476-0.5352-0.0403-0.02330.11810.4871-0.94250.40640.2089-0.28430.62590.0624-0.24310.2275-70.9656-20.232535.7047
84.19550.0238-2.77222.89870.13253.4157-0.47230.582-0.5890.00780.02760.27660.4269-0.49070.44460.1632-0.09050.5489-0.3265-0.11190.175-26.0917-19.544411.2398
96.32090.3039-2.82282.6922-0.4381.70680.01160.98690.02710.0071-0.01360.50440.0432-0.91890.0019-0.02530.13580.53510.52220.01850.1807-77.25872.969926.4151
104.7686-0.2867-2.33741.73350.00392.35460.1961.06460.2126-0.0032-0.13810.1126-0.0919-0.7847-0.05790.14110.00340.48380.1648-0.03880.0845-33.9362-1.5736-0.3474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|7 - 194 }
2X-RAY DIFFRACTION2{ A|195 - 316 }
3X-RAY DIFFRACTION3{ B|7 - 194 }
4X-RAY DIFFRACTION4{ B|195 - 316 }
5X-RAY DIFFRACTION5{ C|7 - 194 }
6X-RAY DIFFRACTION6{ C|195 - 316 }
7X-RAY DIFFRACTION7{ D|7 - 194 }
8X-RAY DIFFRACTION8{ D|195 - 316 }
9X-RAY DIFFRACTION9{ E|7 - 194 }
10X-RAY DIFFRACTION10{ E|195 - 316 }

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