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- PDB-5osa: GLIC-GABAAR alpha1 chimera crystallized at pH4.6 -

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Basic information

Entry
Database: PDB / ID: 5osa
TitleGLIC-GABAAR alpha1 chimera crystallized at pH4.6
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 / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / sodium channel activity / potassium channel activity ...GABA receptor activation / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / sodium channel activity / potassium channel activity / chloride channel complex / extracellular ligand-gated monoatomic ion channel activity / cytoplasmic vesicle membrane / chloride transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / transmembrane signaling receptor activity / dendritic spine / identical protein binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : / 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 / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : / 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 / DODECANE / CHOLESTEROL HEMISUCCINATE / 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: 2.75000236232 Å
AuthorsLaverty, D.C. / Gold, M.G. / Smart, T.G.
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: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Oct 30, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.4Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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,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)197,73833
Polymers193,2215
Non-polymers4,51728
Water63135
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26670 Å2
ΔGint-188 kcal/mol
Surface area61500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.017, 133.947, 162.697
Angle α, β, γ (deg.)90.000, 103.535, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASPASP(chain 'A' and (resid 3 through 48 or resid 50 through 415))AA3 - 483 - 48
12ARGARGTYRTYR(chain 'A' and (resid 3 through 48 or resid 50 through 415))AA50 - 19350 - 193
13GLYGLYALAALA(chain 'A' and (resid 3 through 48 or resid 50 through 415))AA223 - 318194 - 289
14LYSLYSLEULEU(chain 'A' and (resid 3 through 48 or resid 50 through 415))AA390 - 415290 - 315
21METMETASPASP(chain 'B' and (resid 3 through 48 or resid 50...BB3 - 483 - 48
22ARGARGTYRTYR(chain 'B' and (resid 3 through 48 or resid 50...BB50 - 19350 - 193
23GLYGLYALAALA(chain 'B' and (resid 3 through 48 or resid 50...BB223 - 318194 - 289
24LYSLYSLEULEU(chain 'B' and (resid 3 through 48 or resid 50...BB390 - 415290 - 315
31METMETASPASP(chain 'C' and (resid 3 through 48 or resid 50...CC3 - 483 - 48
32ARGARGTYRTYR(chain 'C' and (resid 3 through 48 or resid 50...CC50 - 19350 - 193
33GLYGLYALAALA(chain 'C' and (resid 3 through 48 or resid 50...CC223 - 318194 - 289
34LYSLYSLEULEU(chain 'C' and (resid 3 through 48 or resid 50...CC390 - 415290 - 315
41METMETASPASP(chain 'D' and (resid 3 through 48 or resid 50 through 415))DD3 - 483 - 48
42ARGARGTYRTYR(chain 'D' and (resid 3 through 48 or resid 50 through 415))DD50 - 19350 - 193
43GLYGLYALAALA(chain 'D' and (resid 3 through 48 or resid 50 through 415))DD223 - 318194 - 289
44LYSLYSLEULEU(chain 'D' and (resid 3 through 48 or resid 50 through 415))DD390 - 415290 - 315
51METMETASPASP(chain 'E' and (resid 3 through 48 or resid 50 through 415))EE3 - 483 - 48
52ARGARGTYRTYR(chain 'E' and (resid 3 through 48 or resid 50 through 415))EE50 - 19350 - 193
53GLYGLYALAALA(chain 'E' and (resid 3 through 48 or resid 50 through 415))EE223 - 318194 - 289
54LYSLYSLEULEU(chain 'E' and (resid 3 through 48 or resid 50 through 415))EE390 - 415290 - 315

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Components

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Protein , 1 types, 5 molecules ABCDE

#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 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7NDN8, UniProt: P62812

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Non-polymers , 5 types, 63 molecules

#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.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H26
#5: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C31H50O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 5.48 Å3/Da / Density % sol: 77.54 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM NaCl, 100 mM sodium acetate pH 4.6, 12 % PEG 6000
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: 2.75→95.28 Å / Num. obs: 100157 / % possible obs: 99.48 % / Redundancy: 3.5 % / Biso Wilson estimate: 60.7400653892 Å2 / CC1/2: 0.946 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.066 / Net I/σ(I): 1.2
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4988 / CC1/2: 0.868 / Rpim(I) all: 0.73 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTERdev_2645refinement
PHENIXdev_2645refinement
xia2data processing
PHASERphasing
BUCCANEERmodel building
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HFI

4hfi


Resolution: 2.75000236232→29.9797579828 Å / SU ML: 0.298040544675 / Cross valid method: FREE R-VALUE / σ(F): 1.32870987971 / Phase error: 30.0889651029
RfactorNum. reflection% reflection
Rfree0.228857684594 5028 5.04039938248 %
Rwork0.203369539203 --
obs0.20463086704 99754 99.5668143889 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 89.8610594938 Å2
Refinement stepCycle: LAST / Resolution: 2.75000236232→29.9797579828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12457 0 310 35 12802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051118776811213084
X-RAY DIFFRACTIONf_angle_d0.81266883371617898
X-RAY DIFFRACTIONf_chiral_restr0.04903478657012100
X-RAY DIFFRACTIONf_plane_restr0.004344739951812225
X-RAY DIFFRACTIONf_dihedral_angle_d9.677538118617687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.78120.3911199440351920.3444975922253167X-RAY DIFFRACTION99.1733097136
2.7812-2.81390.3745686613861620.3209789475163121X-RAY DIFFRACTION99.3343419062
2.8139-2.84820.3350341483711690.3130947085823165X-RAY DIFFRACTION99.0787518574
2.8482-2.88420.3133978093481770.3029963889773052X-RAY DIFFRACTION99.109883364
2.8842-2.92220.327144475291780.3045134958483164X-RAY DIFFRACTION99.3755575379
2.9222-2.96220.3297072326251670.2798573892743132X-RAY DIFFRACTION99.3076459964
2.9622-3.00440.3328650992031750.2864580825623145X-RAY DIFFRACTION99.520383693
3.0044-3.04920.3229422919721700.2845262518643095X-RAY DIFFRACTION99.8470948012
3.0492-3.09680.2727819012731620.2600496745523205X-RAY DIFFRACTION99.8813408484
3.0968-3.14760.3060488391221760.2487425125563087X-RAY DIFFRACTION99.5727799817
3.1476-3.20180.3036176502681710.2402938820273172X-RAY DIFFRACTION99.553305539
3.2018-3.25990.262666072551680.2313659003973173X-RAY DIFFRACTION99.5530393325
3.2599-3.32260.3014975866341600.2334984050773100X-RAY DIFFRACTION99.3296770262
3.3226-3.39030.2515973311751970.2347125542543116X-RAY DIFFRACTION99.2510485321
3.3903-3.46390.267722650521760.2355653245493166X-RAY DIFFRACTION99.3755575379
3.4639-3.54430.2715999051431710.2344826821053133X-RAY DIFFRACTION99.7885835095
3.5443-3.63280.2585820195251770.21147975363140X-RAY DIFFRACTION99.3708807669
3.6328-3.73090.2200646369231570.1968834372293139X-RAY DIFFRACTION99.7578692494
3.7309-3.84050.2006362474221610.1874472569463181X-RAY DIFFRACTION99.8804542738
3.8405-3.96410.2033697356061520.1908697054783194X-RAY DIFFRACTION100
3.9641-4.10550.2277818826681610.1786244419883148X-RAY DIFFRACTION99.9395952884
4.1055-4.26940.1992639044671840.1640575032153160X-RAY DIFFRACTION99.880525687
4.2694-4.46310.1785291938541440.1622122699093202X-RAY DIFFRACTION99.8805970149
4.4631-4.69760.1624208676871540.1399977621973184X-RAY DIFFRACTION99.910206525
4.6976-4.99070.1750058345121710.1505228037453175X-RAY DIFFRACTION99.6129800536
4.9907-5.3740.2036044752061510.1681921917043171X-RAY DIFFRACTION99.699879952
5.374-5.9110.2018318445081520.1844210954663199X-RAY DIFFRACTION100
5.911-6.75780.2158708084191500.2015392485973228X-RAY DIFFRACTION99.7637330183
6.7578-8.48210.1851950240781670.1833214740143205X-RAY DIFFRACTION100
8.4821-29.98150.2090291815021760.2186338362523207X-RAY DIFFRACTION98.3716196569
Refinement TLS params.Method: refined / Origin x: 47.5064551016 Å / Origin y: 1.41407561932 Å / Origin z: 26.7417564881 Å
111213212223313233
T0.474402783567 Å20.0675798665437 Å20.0305613785697 Å2-0.450043386015 Å2-0.0216819510558 Å2--0.528687976533 Å2
L0.760952887066 °20.0653086152909 °20.580180143994 °2-0.524685589918 °20.0519566670012 °2--1.4267637436 °2
S0.0320911156957 Å °0.0183470764553 Å °-0.00898994364437 Å °-0.116202281694 Å °-0.0390207097291 Å °0.0808766516708 Å °-0.0456070729424 Å °0.00830701882021 Å °-8.03473689378E-5 Å °
Refinement TLS groupSelection details: all

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