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- PDB-8bhg: GABA-A receptor a5 heteromer - a5V2 - Bretazenil -

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Basic information

Entry
Database: PDB / ID: 8bhg
TitleGABA-A receptor a5 heteromer - a5V2 - Bretazenil
Components(Gamma-aminobutyric acid receptor subunit ...) x 2
KeywordsMEMBRANE PROTEIN / pLGIC GABA Neurotransmission
Function / homology
Function and homology information


benzodiazepine receptor activity / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / inner ear receptor cell development / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / GABA receptor binding ...benzodiazepine receptor activity / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / inner ear receptor cell development / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / GABA receptor binding / innervation / postsynaptic specialization membrane / neurotransmitter receptor activity / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / chloride channel activity / adult behavior / neuronal cell body membrane / cochlea development / Signaling by ERBB4 / associative learning / chloride channel complex / GABA-ergic synapse / regulation of postsynaptic membrane potential / behavioral fear response / chloride transmembrane transport / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / post-embryonic development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / presynaptic membrane / signaling receptor activity / postsynapse / postsynaptic membrane / neuron projection / axon / synapse / signal transduction / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / : / Gamma-aminobutyric-acid A receptor, alpha subunit / 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 ...Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / : / Gamma-aminobutyric-acid A receptor, alpha subunit / 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
Similarity search - Domain/homology
NITRATE ION / Bretazenil / Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsMiller, P.S. / Malinauskas, T.M. / Omari, K.E. / Aricescu, A.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M024709/1 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: The molecular basis of drug selectivity for α5 subunit-containing GABA receptors.
Authors: Vikram Babu Kasaragod / Tomas Malinauskas / Ayla A Wahid / Judith Lengyel / Frederic Knoflach / Steven W Hardwick / Charlotte F Jones / Wan-Na Chen / Xavier Lucas / Kamel El Omari / Dimitri ...Authors: Vikram Babu Kasaragod / Tomas Malinauskas / Ayla A Wahid / Judith Lengyel / Frederic Knoflach / Steven W Hardwick / Charlotte F Jones / Wan-Na Chen / Xavier Lucas / Kamel El Omari / Dimitri Y Chirgadze / A Radu Aricescu / Giuseppe Cecere / Maria-Clemencia Hernandez / Paul S Miller /
Abstract: α5 subunit-containing γ-aminobutyric acid type A (GABA) receptors represent a promising drug target for neurological and neuropsychiatric disorders. Altered expression and function contributes to ...α5 subunit-containing γ-aminobutyric acid type A (GABA) receptors represent a promising drug target for neurological and neuropsychiatric disorders. Altered expression and function contributes to neurodevelopmental disorders such as Dup15q and Angelman syndromes, developmental epilepsy and autism. Effective drug action without side effects is dependent on both α5-subtype selectivity and the strength of the positive or negative allosteric modulation (PAM or NAM). Here we solve structures of drugs bound to the α5 subunit. These define the molecular basis of binding and α5 selectivity of the β-carboline, methyl 6,7-dimethoxy-4-ethyl-β-carboline-3-carboxylate (DMCM), type II benzodiazepine NAMs, and a series of isoxazole NAMs and PAMs. For the isoxazole series, each molecule appears as an 'upper' and 'lower' moiety in the pocket. Structural data and radioligand binding data reveal a positional displacement of the upper moiety containing the isoxazole between the NAMs and PAMs. Using a hybrid molecule we directly measure the functional contribution of the upper moiety to NAM versus PAM activity. Overall, these structures provide a framework by which to understand distinct modulator binding modes and their basis of α5-subtype selectivity, appreciate structure-activity relationships, and empower future structure-based drug design campaigns.
History
DepositionOct 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor subunit alpha-5
B: Gamma-aminobutyric acid receptor subunit gamma-2
C: Gamma-aminobutyric acid receptor subunit alpha-5
D: Gamma-aminobutyric acid receptor subunit alpha-5
E: Gamma-aminobutyric acid receptor subunit alpha-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,36524
Polymers204,3475
Non-polymers6,01719
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.140, 137.637, 113.351
Angle α, β, γ (deg.)90.000, 106.060, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 15 through 75 or resid 77...
d_2ens_1(chain "C" and (resid 15 through 75 or resid 77...
d_3ens_1(chain "D" and (resid 15 through 75 or resid 77...
d_4ens_1(chain "E" and (resid 15 through 75 or resid 77...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILEASPA2 - 62
d_12ens_1ARGLEUA64 - 65
d_13ens_1PHEPROA67 - 70
d_14ens_1GLNGLNA72
d_15ens_1LEUILEA74 - 111
d_16ens_1ASNLEUA113 - 145
d_17ens_1PHETHRA147 - 162
d_18ens_1SERSERA168 - 176
d_19ens_1LEUTHRA178 - 301
d_110ens_1SERASPA303 - 312
d_111ens_1METARGA314 - 316
d_112ens_1VALTYRA318 - 334
d_21ens_1ILEASPC2 - 62
d_22ens_1ARGLEUC64 - 65
d_23ens_1PHEPROC67 - 70
d_24ens_1GLNGLNC72
d_25ens_1LEUILEC74 - 111
d_26ens_1ASNLEUC113 - 145
d_27ens_1PHETHRC147 - 162
d_28ens_1SERSERC168 - 176
d_29ens_1LEUTHRC178 - 301
d_210ens_1SERASPC303 - 312
d_211ens_1METARGC314 - 316
d_212ens_1VALTYRC318 - 334
d_31ens_1ILEASPD1 - 61
d_32ens_1ARGLEUD63 - 64
d_33ens_1PHEPROD66 - 69
d_34ens_1GLNGLND71
d_35ens_1LEUILED73 - 110
d_36ens_1ASNLEUD112 - 144
d_37ens_1PHETHRD146 - 161
d_38ens_1SERSERD167 - 175
d_39ens_1LEUTHRD177 - 300
d_310ens_1SERASPD302 - 311
d_311ens_1METARGD313 - 315
d_312ens_1VALTYRD317 - 333
d_41ens_1ILEASPE2 - 62
d_42ens_1ARGLEUE64 - 65
d_43ens_1PHEPROE67 - 70
d_44ens_1GLNGLNE72
d_45ens_1LEUILEE74 - 111
d_46ens_1ASNLEUE113 - 145
d_47ens_1PHETHRE147 - 162
d_48ens_1SERSERE168 - 176
d_49ens_1LEUTHRE178 - 301
d_410ens_1SERASPE303 - 312
d_411ens_1METARGE314 - 316
d_412ens_1VALTYRE318 - 334

NCS oper:
IDCodeMatrixVector
1given(-0.816753965755, -0.576143146624, -0.0311774601751), (0.575755341408, -0.810293601402, -0.10922484318), (0.0376662483513, -0.107160413054, 0.993528006454)59.0938283512, 43.9556783957, 2.71591499503
2given(-0.809358824686, 0.585622546946, 0.0445480124247), (-0.586778824636, -0.803052435411, -0.103910523714), (-0.0250779556816, -0.110240729716, 0.993588485063)20.3559358657, 69.0509113205, 4.0643571609
3given(0.314329750914, 0.946958959021, 0.0668246782243), (-0.947721947425, 0.31709909776, -0.035654909464), (-0.0549537811231, -0.0521238153721, 0.997127469189)-16.8005361074, 41.7286720745, 2.69822156133

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Components

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Gamma-aminobutyric acid receptor subunit ... , 2 types, 5 molecules ACDEB

#1: Protein
Gamma-aminobutyric acid receptor subunit alpha-5 / GABA(A) receptor subunit alpha-5


Mass: 40148.879 Da / Num. of mol.: 4
Mutation: I79M,T82N,V98I,R101A,S103T,N121D,L123R,L124V,S126D,K127Q,G138D,I142F,N145W,L152M,L155I,E156W,D157N,T160R,L161V,Q176D,A184E,H185Q,A186N,P287A,I336L,T340F,F344I,V335I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRA5 / Production host: Homo sapiens (human) / References: UniProt: P31644
#2: Protein Gamma-aminobutyric acid receptor subunit gamma-2 / GABA(A) receptor subunit gamma-2


Mass: 43751.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRG2 / Production host: Homo sapiens (human) / References: UniProt: P18507

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Sugars , 2 types, 11 molecules

#4: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 22 molecules

#3: Chemical
ChemComp-QMU / Bretazenil / ~{tert}-butyl (7~{S})-14-bromanyl-12-oxidanylidene-2,4,11-triazatetracyclo[11.4.0.0^{2,6}.0^{7,11}]heptadeca-1(17),3,5,13,15-pentaene-5-carboxylate


Mass: 418.284 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H20BrN3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 400 0.37M potassium nitrate 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.39→48.56 Å / Num. obs: 43371 / % possible obs: 91.2 % / Redundancy: 13.3 % / Biso Wilson estimate: 41.25 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.184 / Net I/σ(I): 10.4
Reflection shellResolution: 2.39→2.7 Å / Rmerge(I) obs: 1.132 / Num. unique obs: 428 / CC1/2: 0.596

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4COF

4cof


Resolution: 2.39→48.56 Å / SU ML: 0.3244 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.4728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 2205 5.08 %
Rwork0.2573 41166 -
obs0.2586 43371 91.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.3 Å2
Refinement stepCycle: LAST / Resolution: 2.39→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13556 0 386 14 13956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003314319
X-RAY DIFFRACTIONf_angle_d0.554119499
X-RAY DIFFRACTIONf_chiral_restr0.04012213
X-RAY DIFFRACTIONf_plane_restr0.00352514
X-RAY DIFFRACTIONf_dihedral_angle_d11.36855288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.64293810191
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.605296613968
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.585210087457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.440.493950.386389X-RAY DIFFRACTION1.61
2.45-2.50.4814120.3612252X-RAY DIFFRACTION4.65
2.5-2.560.3799240.3554453X-RAY DIFFRACTION8.18
2.56-2.630.4194320.3497614X-RAY DIFFRACTION10.99
2.63-2.710.3368360.3357763X-RAY DIFFRACTION13.61
2.71-2.80.3876450.3336925X-RAY DIFFRACTION16.58
2.8-2.90.3375460.32471101X-RAY DIFFRACTION19.58
2.9-3.010.3506720.31271386X-RAY DIFFRACTION24.88
3.01-3.150.36461040.34481867X-RAY DIFFRACTION33.57
3.15-3.320.33161660.33082727X-RAY DIFFRACTION49.33
3.32-3.530.31462360.30554136X-RAY DIFFRACTION73.94
3.53-3.80.31782400.26624668X-RAY DIFFRACTION83.85
3.8-4.180.27912660.24095314X-RAY DIFFRACTION94.66
4.18-4.780.23582800.21935607X-RAY DIFFRACTION99.83
4.78-6.030.26053430.22785575X-RAY DIFFRACTION99.97
6.03-48.560.26862980.2495689X-RAY DIFFRACTION99.75
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)
10.3234224695580.0509072858219-0.1776191479730.686057343396-0.05313324688241.463994371570.1971992487-0.1565730397030.189130804913-0.180840018869-0.0844838965670.441215445489-0.106023931624-0.730197672703-0.1648321940090.2257413691040.02786436227660.08893074187360.5949590979190.08125306372670.2732012742217.9241705380530.8786485137256.570259081
20.4161044493390.211365456210.01742592866690.6684937160190.06553294206040.6878183002070.131312695819-0.0555970970201-0.0713726424228-0.117905256509-0.1004043890480.2917297653660.251860238879-0.305694082596-0.07015848765710.807836990102-0.758719062968-0.1057463981060.7908557016440.1258225737120.3846220916554.232600453296.38590579968254.885848329
30.3228377445220.0579872568708-0.01584168165050.2580290582580.2147829452690.4565103391230.154647747359-0.162193999613-0.307199260911-0.00725261390069-0.0330419587388-0.09792635694950.4354108437130.0260173832680.02432536037671.28586029016-0.0917805437558-0.07150662098540.229117178580.1347656383820.37724649871526.2477585711-4.42964344056254.127452043
40.4888128054830.184456924833-0.2249546010020.3671063029670.2263487195310.60424731540.1397706442850.037644602493-0.1578532770290.05030836665540.0594473643009-0.4842884710040.2493850498610.4946702173710.01594017018570.5598624618240.4987658433110.1156737296340.672191043840.01304599502760.37573398446143.610545168712.882978242255.347302257
50.4431803828620.132059747517-0.1413448272270.620972487805-0.04527805699660.936574705370.169111035313-0.1156917522450.18003474825-0.182280300836-0.0226073843561-0.258169272963-0.3031490135260.2522741961770.100504567370.191922858452-0.2866651363960.1128661676660.131420312120.02021939779250.13337939521432.297921818134.8142671953256.585386152
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'D' and resid 15 through 456)DD15 - 4561 - 335
22(chain 'E' and resid 14 through 456)EE14 - 4561 - 336
33(chain 'A' and resid 14 through 456)AA14 - 4561 - 336
44(chain 'B' and resid 23 through 464)BB23 - 4631 - 334
55(chain 'C' and resid 14 through 455)CC14 - 4541 - 334

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