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- PDB-5osc: GLIC-GABAAR alpha1 chimera crystallized in complex with pregnenol... -

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Basic information

Entry
Database: PDB / ID: 5osc
TitleGLIC-GABAAR alpha1 chimera crystallized in complex with pregnenolone sulfate at pH 4.5
ComponentsProton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
KeywordsTRANSPORT PROTEIN / GABAA-receptor ion channel Ion transport Extracellular ligand gated ion channel
Function / homology
Function and homology information


GABA receptor activation / benzodiazepine receptor activity / inhibitory synapse / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic ...GABA receptor activation / benzodiazepine receptor activity / inhibitory synapse / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / sodium channel activity / transmembrane transporter complex / chloride channel complex / potassium channel activity / regulation of postsynaptic membrane potential / presynaptic active zone membrane / dendrite membrane / extracellular ligand-gated monoatomic ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoplasmic vesicle membrane / chloride transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / synaptic vesicle membrane / transmembrane signaling receptor activity / dendritic spine / postsynapse / neuron projection / axon / neuronal cell body / dendrite / synapse / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 2 subunit / : / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : / 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 ...Gamma-aminobutyric-acid A receptor, alpha 2 subunit / : / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : / 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 / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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
Pregnenolone sulfate / ACETATE ION / CHOLESTEROL HEMISUCCINATE / Gamma-aminobutyric acid receptor subunit alpha-2 / Gamma-aminobutyric acid receptor subunit alpha-1 / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLaverty, D.C. / Gold, M.G. / Smart, T.G.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K005537/1 United Kingdom
Royal Society104194/Z/14/Z United Kingdom
Engineering and Physical Sciences Research CouncilEP/J003921/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L000253/1 United Kingdom
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites.
Authors: Laverty, D. / Thomas, P. / Field, M. / Andersen, O.J. / Gold, M.G. / Biggin, P.C. / Gielen, M. / Smart, T.G.
History
DepositionAug 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 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

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Assembly

Deposited unit
A: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
B: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
C: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
D: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
E: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,28728
Polymers193,2215
Non-polymers5,06623
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23280 Å2
ΔGint-174 kcal/mol
Surface area61720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.310, 133.180, 161.860
Angle α, β, γ (deg.)90.00, 102.71, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN 'A' AND (RESID 4 THROUGH 62 OR (RESID 63...
211(CHAIN 'B' AND (RESID 4 THROUGH 60 OR (RESID 61...
311(CHAIN 'C' AND (RESID 4 THROUGH 60 OR (RESID 61...
411CHAIN 'D'
511CHAIN 'E'

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Components

#1: Protein
Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1 / GLIC / Ligand-gated ion channel / LGIC / GABA(A) receptor subunit alpha-2 / GABA(A) receptor subunit alpha-1


Mass: 38644.180 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria), (gene. exp.) Mus musculus (house mouse)
Strain: PCC 7421 / Gene: glvI, glr4197, Gabra2, Gabra-2, Gabra1, Gabra-1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q7NDN8, UniProt: P26048, UniProt: P62812
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-A8W / Pregnenolone sulfate / pregn-5-en-3beta-ol-20-one-3beta-sulfate


Mass: 396.541 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H32O5S / Comment: antidepressant*YM
#5: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C31H50O4

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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: 4.99 Å3/Da / Density % sol: 75.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 12-16% PEG 4000, 100 mM NaCl, 100 mM Li2S04, 100 mM sodium acetate pH 4-5
PH range: 4-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.97→83.52 Å / Num. obs: 77782 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 81.11 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 1
Reflection shellResolution: 2.97→3.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OSA

5osa


Resolution: 3.1→29.92 Å / SU ML: 0.434 / Cross valid method: FREE R-VALUE / σ(F): 1.343 / Phase error: 33.066
RfactorNum. reflection% reflection
Rfree0.246 3421 5.014 %
Rwork0.211 --
obs0.213 68224 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 114.4 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12436 0 347 0 12783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213125
X-RAY DIFFRACTIONf_angle_d0.5318032
X-RAY DIFFRACTIONf_dihedral_angle_d7.8017719
X-RAY DIFFRACTIONf_chiral_restr0.0422135
X-RAY DIFFRACTIONf_plane_restr0.0032235
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
13CX-RAY DIFFRACTIONPOSITIONAL
14DX-RAY DIFFRACTIONPOSITIONAL
15EX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.14430.47971660.41632681X-RAY DIFFRACTION98
3.1443-3.19120.41091550.38112611X-RAY DIFFRACTION99
3.1912-3.2410.3871290.3492745X-RAY DIFFRACTION99
3.241-3.2940.33141510.33642650X-RAY DIFFRACTION99
3.294-3.35080.38731440.32982674X-RAY DIFFRACTION99
3.3508-3.41160.37131320.32352671X-RAY DIFFRACTION99
3.4116-3.47710.35911290.30962724X-RAY DIFFRACTION99
3.4771-3.5480.37931330.28232715X-RAY DIFFRACTION99
3.548-3.6250.30931280.26392667X-RAY DIFFRACTION99
3.625-3.70920.29641620.24472674X-RAY DIFFRACTION99
3.7092-3.80180.2671290.21662723X-RAY DIFFRACTION99
3.8018-3.90440.25151580.20722714X-RAY DIFFRACTION100
3.9044-4.0190.24411470.18592697X-RAY DIFFRACTION100
4.019-4.14840.22321540.17222690X-RAY DIFFRACTION100
4.1484-4.29620.20021280.16152705X-RAY DIFFRACTION99
4.2962-4.46770.18761560.1542687X-RAY DIFFRACTION100
4.4677-4.67030.15411440.13322720X-RAY DIFFRACTION99
4.6703-4.91560.16021410.13572710X-RAY DIFFRACTION99
4.9156-5.2220.19211270.15562714X-RAY DIFFRACTION99
5.222-5.62280.18981340.17642720X-RAY DIFFRACTION99
5.6228-6.18410.2621470.20472722X-RAY DIFFRACTION99
6.1841-7.06860.2581390.20752758X-RAY DIFFRACTION99
7.0686-8.86710.20171400.19822730X-RAY DIFFRACTION99
8.8671-29.92110.2331480.22122701X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 12.0503 Å / Origin y: -21.0137 Å / Origin z: 184.8753 Å
111213212223313233
T0.6781 Å20.0821 Å20.0258 Å2-0.6704 Å2-0.0454 Å2--0.6896 Å2
L0.7895 °20.0022 °20.4522 °2-0.8126 °2-0.0729 °2--1.4825 °2
S0.0285 Å °-0.0534 Å °-0.0249 Å °-0.0059 Å °-0.0719 Å °0.0193 Å °-0.0441 Å °0.0548 Å °0.0315 Å °
Refinement TLS groupSelection details: ALL

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