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

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Basic information

Entry
Database: PDB / ID: 6fvq
TitleThe active form of a pentameric ion channel (sTeLIC) gated by alkaline pH - R86A
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: 3.3 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
DepositionMar 5, 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)188,62715
Polymers186,1245
Non-polymers2,50310
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30030 Å2
ΔGint-44 kcal/mol
Surface area60930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.237, 112.475, 144.461
Angle α, β, γ (deg.)90.00, 113.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 37224.707 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) endosymbiont of Tevnia jerichonana (vent Tica) (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

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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: 4.31 Å3/Da / Density % sol: 71.45 %
Crystal growTemperature: 291 K / Method: evaporation / Details: 150mM MgCl2 35%PEG200 Tris pH 8.0 3% DMSO

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.3→49.15 Å / Num. obs: 47694 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 87.39 Å2 / Net I/σ(I): 8.8
Reflection shellResolution: 3.3→3.42 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.461
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1697 4.88 %RANDOM
Rwork0.204 ---
obs0.205 34747 73 %-
Displacement parametersBiso mean: 71.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.9657 Å20 Å2-0.0112 Å2
2---5.5035 Å20 Å2
3----1.4622 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: 1 / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12755 0 170 0 12925
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113280HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0917995HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4550SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes300HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1900HARMONIC5
X-RAY DIFFRACTIONt_it13280HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion19.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1700SEMIHARMONIC5
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_contact14538SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.4 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2709 -4.92 %
Rwork0.2393 1082 -
all0.2408 1138 -
obs--27.75 %
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)
12.64550.1633-1.99660.2195-0.16952.35010.1280.29310.41040.13370.04090.1712-0.2402-0.2611-0.16890.06560.12510.1777-0.28060.09290.099155.397520.131628.2578
24.64470.4767-2.91590.5215-0.59242.5810.1359-0.47520.18420.3121-0.0270.1185-0.14060.3853-0.10890.0962-0.09270.0652-0.2428-0.1665-0.169568.036911.412447.3102
33.78150.4401-2.06480.612-0.10081.6135-0.1355-0.4785-0.27850.2499-0.03730.10610.26310.31530.17270.08480.05130.0765-0.2240.1276-0.12467.2552-13.051446.2413
43.95650.0993-2.25210.28480.16691.9905-0.17050.4355-0.31470.0559-0.04650.19110.3404-0.35990.2170.0203-0.11160.1488-0.2632-0.12360.089954.2517-19.446126.5579
52.9545-0.5609-2.04490.87260.41361.6064-0.01980.46970.042-0.0433-0.00170.2323-0.0052-0.38770.0215-0.22250.0558-0.10350.23220.0203-0.247746.87731.089215.3578
6-1.6350.03171.4930.2479-0.01551.6350.0263-0.0106-0.0334-0.0064-0.01190.0082-0.0311-0.0093-0.0144-0.015-0.012-0.03950.00870.00950.053187.63150.013413.4039
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|* }
6X-RAY DIFFRACTION6{ F|* }

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