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- PDB-4qh1: The GLIC pentameric Ligand-Gated Ion Channel (wild-type) in compl... -

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Basic information

Entry
Database: PDB / ID: 4qh1
TitleThe GLIC pentameric Ligand-Gated Ion Channel (wild-type) in complex with bromoacetate
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / membrane
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium 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
BROMIDE ION / bromoacetic acid / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsFourati, Z. / Delarue, M. / Sauguet, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural characterization of potential modulation sites in the extracellular domain of the prokaryotic pentameric proton-gated ion channel GLIC
Authors: Fourati, Z. / Delarue, M. / Sauguet, L.
History
DepositionMay 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)182,91521
Polymers181,1035
Non-polymers1,81216
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22990 Å2
ΔGint-154 kcal/mol
Surface area62240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.431, 134.021, 158.861
Angle α, β, γ (deg.)90.00, 101.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 36220.672 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus PCC 7421 (bacteria)
Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-BXA / bromoacetic acid / Bromoacetic acid


Mass: 138.948 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3BrO2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 5.22 Å3/Da / Density % sol: 76.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 400 mM Sodium Isothiocyanate, 100 mM Sodium acetate, 16% glycerol, 12-15% PEG4000 2% DMSO, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9191 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 3.39→49.4 Å / Num. all: 317163 / Num. obs: 100895 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 94.55 Å2
Reflection shellResolution: 3.39→3.57 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMACrefinement
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.8964 / Cor.coef. Fo:Fc free: 0.8911 / SU R Cruickshank DPI: 8.112 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 2593 5.08 %RANDOM
Rwork0.2022 ---
obs0.2033 51007 99.9 %-
all-51007 --
Displacement parametersBiso mean: 120.08 Å2
Baniso -1Baniso -2Baniso -3
1--15.1756 Å20 Å230.3243 Å2
2---9.4581 Å20 Å2
3---24.6337 Å2
Refine analyzeLuzzati coordinate error obs: 0.795 Å
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12625 0 56 9 12690
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113045HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0117840HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4320SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes261HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1892HARMONIC5
X-RAY DIFFRACTIONt_it13045HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion17.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1761SEMIHARMONIC5
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_contact14953SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3013 205 5.45 %
Rwork0.2731 3554 -
all0.2746 3759 -
obs--99.9 %
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)
12.24430.11341.95421.2863-0.19414.0227-0.0667-0.10430.1302-0.05460.11630.1035-0.4612-0.2937-0.04960.16870.168-0.2462-0.3538-0.0358-0.221840.348-6.602429.6105
22.73390.23882.86330.94120.36154.25530.0841-0.1164-0.10680.00160.02110.2102-0.1419-0.3923-0.1053-0.07310.0413-0.2303-0.0523-0.0001-0.176228.3742-27.965335.6136
31.55730.27391.61331.63320.59163.41180.2664-0.0729-0.3602-0.1258-0.04340.17050.3564-0.295-0.2230.00530.0549-0.3016-0.2818-0.0524-0.133342.2951-47.613928.6465
41.38190.08471.50461.0498-0.03634.9377-0.00170.2078-0.1625-0.2425-0.0027-0.0791-0.14360.43020.00450.08410.2079-0.2644-0.2158-0.1278-0.223663.1223-38.549117.6516
50.8949-0.35950.95241.1015-0.79443.9162-0.02880.1520.0818-0.2441-0.0063-0.0994-0.16140.29750.03520.1789-0.0877-0.2459-0.22960.0446-0.212961.8866-13.146918.3099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 315
2X-RAY DIFFRACTION2{ B|* }B5 - 315
3X-RAY DIFFRACTION3{ C|* }C5 - 315
4X-RAY DIFFRACTION4{ D|* }D5 - 315
5X-RAY DIFFRACTION5{ E|* }E5 - 315

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