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- PDB-4cof: Crystal structure of a human gamma-aminobutyric acid receptor, th... -

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Basic information

Entry
Database: PDB / ID: 4cof
TitleCrystal structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3 homopentamer
ComponentsGAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-3
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


circadian sleep/wake cycle, REM sleep / reproductive behavior / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex ...circadian sleep/wake cycle, REM sleep / reproductive behavior / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / innervation / response to anesthetic / postsynaptic specialization membrane / inhibitory postsynaptic potential / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / cellular response to zinc ion / exploration behavior / motor behavior / roof of mouth development / Signaling by ERBB4 / cochlea development / social behavior / chloride channel complex / chloride transmembrane transport / cytoplasmic vesicle membrane / cerebellum development / learning / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / memory / dendritic spine / postsynaptic membrane / response to xenobiotic stimulus / cell surface / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Gamma-aminobutyric-acid A receptor, beta 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 ...Neurotransmitter-gated ion-channel transmembrane domain / Gamma-aminobutyric-acid A receptor, beta 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
BENZAMIDINE / Gamma-aminobutyric acid receptor subunit beta-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsMiller, P.S. / Aricescu, A.R.
CitationJournal: Nature / Year: 2014
Title: Crystal Structure of a Human Gabaa Receptor
Authors: Miller, P.S. / Aricescu, A.R.
History
DepositionJan 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Structure summary
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Aug 27, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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 BETA-3
B: GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-3
C: GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-3
D: GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-3
E: GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,19826
Polymers204,1605
Non-polymers5,03821
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34230 Å2
ΔGint-128.9 kcal/mol
Surface area65390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.100, 108.900, 207.440
Angle α, β, γ (deg.)90.00, 107.43, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.396, 0.8897, 0.2272), (-0.8922, 0.3144, 0.3243), (0.2171, -0.3311, 0.9183)-28.9186, -42.9619, 10.3559
2given(-0.5846, 0.5577, 0.5893), (-0.5624, -0.802, 0.2012), (0.5848, -0.2138, 0.7825)-76.73, -27.97, 28.29
3given(-0.5915, -0.5552, 0.5847), (0.5499, -0.8081, -0.2111), (0.5897, 0.1966, 0.7833)-76.88, 25.9, 28.46
4given(0.3855, -0.8947, 0.2257), (0.8936, 0.301, -0.3329), (0.2299, 0.33, 0.9155)-30.55, 42.87, 11.43

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Components

#1: Protein
GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-3 / GABA(A) RECEPTOR SUBUNIT BETA-3 / GABA RECEPTOR / IONOTROPIC / BETA-3


Mass: 40831.957 Da / Num. of mol.: 5 / Fragment: RESIDUES 26-312,447-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293S GNTI- / Production host: HOMO SAPIENS (human) / References: UniProt: P28472
#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H8N2
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
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
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
Has protein modificationY

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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: 4.59 Å3/Da / Density % sol: 74 % / Description: NONE
Crystal growpH: 6.5
Details: 11.5% PEG4000 100 MM SODIUM CHLORIDE, 100 MM LITHIUM SULPHATE, 100 MM N-2-ACETAMIDO-IMINODIACETIC ACID, PH 6.5, 2% (W/V) BENZAMIDINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.97→99 Å / Num. obs: 76360 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 83.39 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2.97→3.05 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RHW

3rhw


Resolution: 2.97→40 Å / Cor.coef. Fo:Fc: 0.8744 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.503 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.45 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.286
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 3835 5.02 %RANDOM
Rwork0.2053 ---
obs0.2064 76328 99.76 %-
Displacement parametersBiso mean: 102.12 Å2
Baniso -1Baniso -2Baniso -3
1--10.6452 Å20 Å217.9062 Å2
2---24.165 Å20 Å2
3---34.8102 Å2
Refine analyzeLuzzati coordinate error obs: 0.494 Å
Refinement stepCycle: LAST / Resolution: 2.97→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13643 0 329 0 13972
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114364HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0619588HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6453SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2099HARMONIC5
X-RAY DIFFRACTIONt_it14364HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion3.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1934SEMIHARMONIC5
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_contact16013SEMIHARMONIC4
LS refinement shellResolution: 2.97→3.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2809 266 4.75 %
Rwork0.2343 5333 -
all0.2364 5599 -
obs--99.76 %
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)
11.1868-0.2868-0.52090.7303-0.07542.98610.14650.0056-0.2299-0.0769-0.08550.03840.5273-0.5487-0.0610.1848-0.1525-0.1001-0.1029-0.1456-0.1731-4.8047-23.8317120.8487
21.74110.06680.81231.3351-0.49642.5186-0.0094-0.0311-0.19170.0056-0.0892-0.0020.4027-0.17540.09860.1507-0.0728-0.038-0.0791-0.0356-0.13179.718-19.0774172.9785
31.1743-0.19990.45162.3396-0.12174.05970.01310.1937-0.0136-0.2602-0.0694-0.05610.21510.48160.0563-0.0030.0410.0616-0.0291-0.0769-0.178416.4866-9.7636114.2808
41.65010.24310.61371.38380.7022.0426-0.07210.1889-0.04530.0111-0.0336-0.16130.20860.32890.10570.07320.0758-0.02080.05-0.0287-0.148229.3199-11.9511165.79
52.3308-0.57390.39081.2189-0.33933.0139-0.04570.33490.0761-0.1172-0.13340.0508-0.3797-0.00690.17910.1598-0.0748-0.1059-0.13130.093-0.187910.607216.4319116.4461
61.02810.27950.52741.14791.05233.6032-0.0628-0.00130.1924-0.1309-0.0975-0.0274-0.27360.29480.16030.1101-0.0761-0.0815-0.03030.0817-0.123529.007810.1735165.9037
72.48390.39840.81751.93630.35141.5102-0.13940.2350.1713-0.0979-0.11140.0927-0.3987-0.51180.2508-0.0060.2924-0.18370.1084-0.0924-0.2371-14.511618.6308125.8141
80.79650.1386-0.49851.57940.17491.9241-0.03540.02220.18130.067-0.08060.0692-0.3403-0.25750.1160.10160.1542-0.1169-0.0178-0.0572-0.12329.119816.8524173.1292
91.6532-0.20350.96062.15891.37082.4893-0.0054-0.1673-0.0675-0.25460.06050.1274-0.0372-0.5978-0.0552-0.2798-0.1268-0.06540.3977-0.0623-0.2936-24.2739-6.2554129.2067
101.42570.05430.68911.241-0.16942.9432-0.0922-0.12580.04530.0697-0.02240.12690.1092-0.4160.1146-0.0724-0.0148-0.04740.1902-0.0519-0.1424-2.7231-1.3601177.5875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|217 }
2X-RAY DIFFRACTION2{ A|218 - A|447 }
3X-RAY DIFFRACTION3{ B|10 - B|217 }
4X-RAY DIFFRACTION4{ B|218 - B|447 }
5X-RAY DIFFRACTION5{ C|10 - C|217 }
6X-RAY DIFFRACTION6{ C|218 - C|447 }
7X-RAY DIFFRACTION7{ D|10 - D|217 }
8X-RAY DIFFRACTION8{ D|218 - D|448 }
9X-RAY DIFFRACTION9{ E|10 - E|217 }
10X-RAY DIFFRACTION10{ E|218 - E|447 }

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