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- PDB-4x5t: alpha 1 glycine receptor transmembrane structure fused to the ext... -

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Basic information

Entry
Database: PDB / ID: 4x5t
Titlealpha 1 glycine receptor transmembrane structure fused to the extracellular domain of GLIC
ComponentsProton-gated ion channel,GLRA1 protein,GLRA1 protein
KeywordsSIGNALING PROTEIN / Cys-loop / receptor pentameric / glycine receptor / transmembrane receptor
Function / homology
Function and homology information


transmitter-gated monoatomic ion channel activity / sodium channel activity / glycine binding / chloride channel activity / extracellular ligand-gated monoatomic ion channel activity / plasma membrane => GO:0005886 / potassium channel activity / chloride channel complex / cell projection / transmembrane signaling receptor activity ...transmitter-gated monoatomic ion channel activity / sodium channel activity / glycine binding / chloride channel activity / extracellular ligand-gated monoatomic ion channel activity / plasma membrane => GO:0005886 / potassium channel activity / chloride channel complex / cell projection / transmembrane signaling receptor activity / postsynaptic membrane / identical protein binding / plasma membrane
Similarity search - Function
Glycine receptor alpha / 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, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Glycine receptor alpha / 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, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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
ACETATE ION / NICKEL (II) ION / GLRA1 protein / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSauguet, L. / Corringer, P.J. / Huon, C. / Delarue, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Allosteric and hyperekplexic mutant phenotypes investigated on an alpha 1 glycine receptor transmembrane structure.
Authors: Moraga-Cid, G. / Sauguet, L. / Huon, C. / Malherbe, L. / Girard-Blanc, C. / Petres, S. / Murail, S. / Taly, A. / Baaden, M. / Delarue, M. / Corringer, P.J.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Proton-gated ion channel,GLRA1 protein,GLRA1 protein
B: Proton-gated ion channel,GLRA1 protein,GLRA1 protein
C: Proton-gated ion channel,GLRA1 protein,GLRA1 protein
D: Proton-gated ion channel,GLRA1 protein,GLRA1 protein
E: Proton-gated ion channel,GLRA1 protein,GLRA1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,25822
Polymers189,3985
Non-polymers86017
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20940 Å2
ΔGint-205 kcal/mol
Surface area67680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.894, 132.304, 190.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Proton-gated ion channel,GLRA1 protein,GLRA1 protein / GLIC / Ligand-gated ion channel / LGIC


Mass: 37879.629 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria), (gene. exp.) Homo sapiens (human)
Strain: PCC 7421 / Gene: glvI, glr4197, GLRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8, UniProt: Q14C71
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 16 % PEG 2000MME, 50 mM NiCl2, 4% DMSO, 11% ethylene glycol and 0.1 M NaAcetate pH 3.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 3.5→49.42 Å / Num. obs: 38553 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 127.53 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.036 / Net I/σ(I): 12.8
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 5 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 0.638 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HFI

4hfi


Resolution: 3.5→25 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.8845 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1935 5.04 %RANDOM
Rwork0.2535 ---
obs0.2543 38364 99.85 %-
Displacement parametersBiso mean: 185.99 Å2
Baniso -1Baniso -2Baniso -3
1--3.9629 Å20 Å20 Å2
2--13.2831 Å20 Å2
3----9.3201 Å2
Refine analyzeLuzzati coordinate error obs: 1.016 Å
Refinement stepCycle: LAST / Resolution: 3.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11448 0 32 0 11480
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111700HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1615998HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3777SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes223HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1749HARMONIC5
X-RAY DIFFRACTIONt_it11700HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion20.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1653SEMIHARMONIC5
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_contact12709SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.6 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.225 147 5.04 %
Rwork0.2407 2770 -
all0.2399 2917 -
obs--99.85 %
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)
10.98850.5724-1.5731.3386-0.10800.0151-0.2290.0815-0.41650.03180.5135-0.0430.314-0.04690.3318-0.0096-0.304-0.17290.082-0.1705-74.98641.966216.5116
20.9525-1.2845-1.6180.7591-1.182400.0303-0.1938-0.3526-0.3326-0.01480.3916-0.14940.1746-0.01550.1607-0.24620.3040.5504-0.1332-0.6032-30.8394-1.9309-5.3404
31.12680.3964-0.570900.70730.6159-0.0653-0.2910.2054-0.40550.03710.32610.05680.28540.02810.27690.02160.0181-0.49420.17730.1555-64.573722.566732.4548
44.2313-1.2489-5.82081.11881.77513.1932-0.03030.1494-0.2357-0.1328-0.06670.1562-0.22590.07320.097-0.1503-0.3040.3040.2550.304-0.1009-24.165315.94145.1322
51.3628-0.6124-0.98670.6899-0.43060-0.24810.18150.15070.34170.0501-0.24630.0523-0.16660.1980.2548-0.0199-0.1018-0.3256-0.09660.0727-50.975511.079553.9346
61.64180.0446-3.24790.33460.23171.3671-0.03710.1102-0.21150.2223-0.0299-0.2393-0.5962-0.08970.067-0.5999-0.30230.3040.1230.07420.5622-13.145610.029222.4371
70.36620.6449-1.24210.91710.79180-0.19890.2638-0.29180.3746-0.1156-0.4036-0.229-0.32110.31450.26050.0531-0.0918-0.35630.04420.0727-52.9381-16.733351.2766
80.72211.0552-3.63690.8475-0.52141.51250.07880.1801-0.06250.362-0.0838-0.2535-0.0580.21030.0049-0.51790.27520.304-0.0290.01240.604-12.8637-11.521322.9709
90.31040.39710.05840-0.20371.06340.12460.1333-0.07610.08570.08050.08970.0560.09-0.20510.372-0.0712-0.0252-0.4209-0.16650.0096-67.6665-22.443528.2536
106.2101-0.1725-5.58870.10740.456800.1386-0.074-0.20310.3913-0.24-0.2735-0.00860.02260.10140.06120.1320.3040.2813-0.304-0.286-24.1311-18.86296.5577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|5 - A|189 }
2X-RAY DIFFRACTION2{ A|190 - A|411 }
3X-RAY DIFFRACTION3{ B|5 - B|189 }
4X-RAY DIFFRACTION4{ B|190 - B|411 }
5X-RAY DIFFRACTION5{ C|5 - C|189 }
6X-RAY DIFFRACTION6{ C|190 - C|411 }
7X-RAY DIFFRACTION7{ D|5 - D|189 }
8X-RAY DIFFRACTION8{ D|190 - D|411 }
9X-RAY DIFFRACTION9{ E|5 - E|189 }
10X-RAY DIFFRACTION10{ E|190 - E|411 }

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