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

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Basic information

Entry
Database: PDB / ID: 6fvs
TitleThe active form of a pentameric ion channel (sTeLIC) gated by alkaline pH - sTeLIC in complex with Barium ions (Ba2+)
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: 3.2 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
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)188,42613
Polymers186,5545
Non-polymers1,8728
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27280 Å2
ΔGint-60 kcal/mol
Surface area61650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.840, 112.110, 144.080
Angle α, β, γ (deg.)90.00, 112.79, 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 (vent Tica) (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-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 292 K / Method: evaporation / Details: 150 mM MaCl2 20 mM tris 8.0 35% PEG 200

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 2 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 3.2→49.07 Å / Num. obs: 52251 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 76.99 Å2 / Net I/σ(I): 9.1
Reflection shellResolution: 3.2→3.3 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.407
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2119 4.9 %RANDOM
Rwork0.208 ---
obs0.209 43274 81.8 %-
Displacement parametersBiso mean: 63.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.3196 Å20 Å23.9401 Å2
2--0.0986 Å20 Å2
3----0.4182 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: 1 / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12805 0 108 187 13100
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113275HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1618012HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4539SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes295HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1914HARMONIC5
X-RAY DIFFRACTIONt_it13275HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion19.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1704SEMIHARMONIC5
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_contact14834SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2871 -4.95 %
Rwork0.2592 1729 -
all0.2607 1819 -
obs--46.95 %
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)
10.85720.2554-1.12730.9943-0.19961.4332-0.00570.87180.0771-0.0907-0.0260.2699-0.0647-0.62320.0317-0.40520.1335-0.15020.6079-0.0128-0.3547-60.22090.469915.5009
23.0050.4499-2.11140.3747-0.36172.23580.32710.47250.51170.0664-0.06890.1625-0.4813-0.3073-0.25820.04140.24290.2415-0.23620.20670.0925-51.638619.049928.4837
34.77190.3631-2.810.6317-0.32672.38730.2696-0.71720.30990.2891-0.01960.0558-0.31750.5809-0.250.06-0.11140.0579-0.1339-0.1454-0.1216-39.09939.994947.1678
43.97640.0811-2.32970.65860.14671.8454-0.1419-0.618-0.53690.2941-0.07650.09030.26530.46250.21840.03020.07460.064-0.10230.1855-0.07-40.1066-14.205245.7877
53.6495-0.4156-2.36850.37190.15352.378-0.21380.6237-0.49990.0081-0.0520.16880.3516-0.45350.2658-0.0947-0.19810.1716-0.1685-0.28190.1176-53.1502-20.136426.2436
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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