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- PDB-5osb: GLIC-GABAAR alpha1 chimera crystallized in complex with THDOC at pH4.5 -

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Basic information

Entry
Database: PDB / ID: 5osb
TitleGLIC-GABAAR alpha1 chimera crystallized in complex with THDOC at pH4.5
ComponentsProton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-1,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 / diazepam binding / GABA receptor complex / organic cyclic compound binding / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex ...GABA receptor activation / diazepam binding / GABA receptor complex / organic cyclic compound binding / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / sodium channel activity / neurotransmitter receptor activity / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / chloride channel complex / GABA-ergic synapse / regulation of postsynaptic membrane potential / chloride transmembrane transport / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / transmembrane signaling receptor activity / postsynapse / neuron projection / synapse / identical protein binding / plasma membrane
Similarity search - Function
: / 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, conserved site / Neurotransmitter-gated ion-channels signature. ...: / 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, 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
Tetrahydrodeoxycorticosterone / ACETATE ION / 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: 3.8 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)195,25917
Polymers193,2215
Non-polymers2,03912
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21590 Å2
ΔGint-144 kcal/mol
Surface area61260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.218, 133.507, 162.263
Angle α, β, γ (deg.)90.00, 103.41, 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 3 THROUGH 58 OR RESID 62 THROUGH 415))
211(CHAIN 'B' AND (RESID 3 THROUGH 58 OR RESID 62 THROUGH 415))
311(CHAIN 'C' AND (RESID 3 THROUGH 277 OR (RESID 278...
411(CHAIN 'D' AND (RESID 3 THROUGH 58 OR RESID 62 THROUGH 415))
511(CHAIN 'E' AND (RESID 3 THROUGH 58 OR RESID 62 THROUGH 415))

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Components

#1: Protein
Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1 / GLIC / Ligand-gated ion channel / LGIC / GABA(A) receptor subunit alpha-1 / 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, Gabra1, Gabra-1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7NDN8, UniProt: P62812
#2: Chemical
ChemComp-A8Z / Tetrahydrodeoxycorticosterone / Tetrahydrodeoxycorticosterone


Mass: 334.493 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C21H34O3 / Comment: hormone*YM
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 5.47 Å3/Da / Density % sol: 77.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 12-16% PEG4000, 100mM NaCl, 100 mM Li2SO4, 100mM sodium acetate pH4-4.5
PH range: 4-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.8→95.03 Å / Num. obs: 37899 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 92.29 Å2 / Rmerge(I) obs: 0.1847 / Net I/σ(I): 4.6
Reflection shellResolution: 3.8→3.97 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: 3.8→29.98 Å / SU ML: 0.342 / Cross valid method: FREE R-VALUE / σ(F): 1.336 / Phase error: 40.341
RfactorNum. reflection% reflection
Rfree0.29 1890 5.126 %
Rwork0.241 --
obs0.244 36869 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 190.5 Å2
Refinement stepCycle: LAST / Resolution: 3.8→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12419 0 142 0 12561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00112893
X-RAY DIFFRACTIONf_angle_d0.43217691
X-RAY DIFFRACTIONf_dihedral_angle_d9.1257630
X-RAY DIFFRACTIONf_chiral_restr0.0392097
X-RAY DIFFRACTIONf_plane_restr0.0032212
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 (%)
3.8006-3.89550.45361170.44262450X-RAY DIFFRACTION96
3.8955-4.00060.39721270.36042461X-RAY DIFFRACTION97
4.0006-4.1180.32821280.30892486X-RAY DIFFRACTION97
4.118-4.25060.34181360.27472475X-RAY DIFFRACTION97
4.2506-4.40210.30641480.24132526X-RAY DIFFRACTION97
4.4021-4.57770.23661380.20472443X-RAY DIFFRACTION97
4.5777-4.78530.24721260.16412495X-RAY DIFFRACTION96
4.7853-5.03640.2261380.16312427X-RAY DIFFRACTION96
5.0364-5.35030.22721230.17982449X-RAY DIFFRACTION95
5.3503-5.76070.21461520.17292516X-RAY DIFFRACTION98
5.7607-6.33550.21391420.19212539X-RAY DIFFRACTION98
6.3355-7.2410.29471300.21942532X-RAY DIFFRACTION99
7.241-9.08060.26621280.2392594X-RAY DIFFRACTION100
9.0806-29.97910.33341570.27752586X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 10.0609 Å / Origin y: -19.1505 Å / Origin z: 184.5025 Å
111213212223313233
T2.1504 Å20.1537 Å2-0.5803 Å2-1.4265 Å2-0.0553 Å2--1.3261 Å2
L0.9315 °20.2124 °20.8066 °2-0.5343 °20.1238 °2--1.9005 °2
S0.0417 Å °-0.1891 Å °-0.0056 Å °0.2526 Å °0.0092 Å °-0.1577 Å °0.0435 Å °0.3117 Å °0 Å °
Refinement TLS groupSelection details: ALL

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