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- PDB-9g2d: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the ... -

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Basic information

Entry
Database: PDB / ID: 9g2d
TitleCryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state (C5) sprayed with PBS
ComponentsGamma-aminobutyric acid receptor subunit beta-3
KeywordsMEMBRANE PROTEIN / GABA / neurotransmission / gating cycle / time-resolved cryo-EM
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 / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly ...circadian sleep/wake cycle, REM sleep / reproductive behavior / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / 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 / cochlea development / Signaling by ERBB4 / social behavior / chloride channel complex / cytoplasmic vesicle membrane / chloride transmembrane transport / 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
Gamma-aminobutyric-acid A receptor, beta 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 ...Gamma-aminobutyric-acid A receptor, beta 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
Gamma-aminobutyric acid receptor subunit beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMihaylov, D.B. / Malinauskas, T. / Aricescu, A.R.
Funding support United Kingdom, United States, 6items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
Cancer Research UKDRCRPG-May23/100002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_EX_MR/T046279/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01-GM135550 United States
National Science Foundation (NSF, United States)NeuroNex 2014862 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state (C5) sprayed with PBS
Authors: Mihaylov, D.B. / Malinauskas, T. / Aricescu, A.R.
History
DepositionJul 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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)236,17625
Polymers228,2165
Non-polymers7,95920
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "E"
d_4ens_1chain "D"
d_5ens_1chain "A"
d_1ens_2chain "e"
d_2ens_2chain "b"
d_3ens_2chain "c"
d_4ens_2chain "d"
d_5ens_2chain "a"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNVALVALCC4 - 44758 - 394
d_21ens_1ASNASNVALVALBB4 - 44758 - 394
d_31ens_1ASNASNVALVALEE4 - 44758 - 394
d_41ens_1ASNASNVALVALDD4 - 44758 - 394
d_51ens_1ASNASNVALVALAA4 - 44758 - 394
d_11ens_2NAGNAGNAGNAGeN1
d_12ens_2NAGNAGNAGNAGeN2
d_13ens_2BMABMABMABMAeN3
d_14ens_2MANMANMANMANeN4
d_15ens_2MANMANMANMANeN5
d_16ens_2NAGNAGNAGNAGJO1
d_17ens_2NAGNAGNAGNAGJO2
d_18ens_2NAGNAGNAGNAGEY502
d_21ens_2NAGNAGNAGNAGbH1
d_22ens_2NAGNAGNAGNAGbH2
d_23ens_2BMABMABMABMAbH3
d_24ens_2MANMANMANMANbH4
d_25ens_2MANMANMANMANbH5
d_26ens_2NAGNAGNAGNAGGI1
d_27ens_2NAGNAGNAGNAGGI2
d_28ens_2NAGNAGNAGNAGBR501
d_31ens_2NAGNAGNAGNAGcJ1
d_32ens_2NAGNAGNAGNAGcJ2
d_33ens_2BMABMABMABMAcJ3
d_34ens_2MANMANMANMANcJ4
d_35ens_2MANMANMANMANcJ5
d_36ens_2NAGNAGNAGNAGHK1
d_37ens_2NAGNAGNAGNAGHK2
d_38ens_2NAGNAGNAGNAGCT501
d_41ens_2NAGNAGNAGNAGdL1
d_42ens_2NAGNAGNAGNAGdL2
d_43ens_2BMABMABMABMAdL3
d_44ens_2MANMANMANMANdL4
d_45ens_2MANMANMANMANdL5
d_46ens_2NAGNAGNAGNAGIM1
d_47ens_2NAGNAGNAGNAGIM2
d_48ens_2NAGNAGNAGNAGDW502
d_51ens_2NAGNAGNAGNAGaF1
d_52ens_2NAGNAGNAGNAGaF2
d_53ens_2BMABMABMABMAaF3
d_54ens_2MANMANMANMANaF4
d_55ens_2MANMANMANMANaF5
d_56ens_2NAGNAGNAGNAGFG1
d_57ens_2NAGNAGNAGNAGFG2
d_58ens_2NAGNAGNAGNAGAP501

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.309007401933, -0.951059623008, 0.000137967219673), (0.951059583662, 0.309007429381, 0.00027733073109), (-0.000306390956449, 4.55177978104E-5, 0.999999952026)296.295610848, -46.9823334307, 0.0573248284742
2given(-0.810226667398, 0.586116370736, -0.00058939988032), (-0.586116601282, -0.810226643284, 0.000340902363142), (-0.000277739030723, 0.000621665240246, 0.999999768197)221.036415466, 432.346404566, -0.041948580519
3given(0.308063165235, 0.951365796062, 0.000456407916257), (-0.951365836128, 0.308063290567, -0.000234207578273), (-0.000363419603671, -0.000362060170981, 0.999999868419)-46.8784685511, 296.607428949, 0.138199323012
4given(-0.808529559731, -0.588455558797, 7.97607021481E-5), (0.588455541747, -0.808529484006, 0.000385851085379), (-0.000162567336708, 0.000358907635376, 0.999999922379)432.534766967, 220.078120707, -0.0152446614557
5given(-0.808130917322, 0.589002875265, 0.000182751939624), (-0.589002869409, -0.808130937234, 9.00690637846E-5), (0.000200738433792, -3.48538216903E-5, 0.999999979245)220.012707074, 432.560723867, -0.0276476044033
6given(-0.809511473189, -0.587104057872, -2.47685494687E-6), (0.587104047911, -0.809511460217, 0.000180844532245), (-0.00010817960119, 0.00014494155215, 0.999999983645)432.502764939, 220.538847318, -0.00974298030573
7given(0.308504937075, -0.951222510102, 0.000663381211949), (0.951222739665, 0.30850490388, -0.00015435574885), (-5.78296941583E-5, 0.000678642804458, 0.99999976805)296.316607786, -46.8512351734, -0.110327401556
8given(0.309225408906, 0.950988743898, 0.000235510889194), (-0.950988772189, 0.309225409743, 3.3768940493E-5), (-4.07120689077E-5, -0.000234410425784, 0.999999971697)-46.9967524403, 296.269279375, 0.0434138594026

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Gamma-aminobutyric acid receptor subunit beta-3 / GABA(A) receptor subunit beta-3 / GABAAR subunit beta-3


Mass: 45643.246 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRB3 / Plasmid: pHLsec / Cell line (production host): EXPI 293F / Production host: Homo sapiens (human) / References: UniProt: P28472

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Sugars , 3 types, 15 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 5 / 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 , 2 types, 255 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state (C5) sprayed with PBS
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: EXPI 293F / Plasmid: pHLsec
Buffer solutionpH: 7.4 / Details: 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMsodium chlorideNaCl1
22.7 mMpotassium chlorideKCl1
34.3 mMDisodium phosphateNa2HPO1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: current: 30mA / Grid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Calibrated magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.43 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 601
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9PHENIXdev_5294model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 301423
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21000 / Symmetry type: POINT
Atomic model buildingB value: 60 / Protocol: OTHER / Space: REAL / Target criteria: FSC at 0.5
Atomic model buildingPDB-ID: 7A5V

7a5v


Accession code: 7A5V / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.96 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002114675
ELECTRON MICROSCOPYf_angle_d0.409519980
ELECTRON MICROSCOPYf_chiral_restr0.03982360
ELECTRON MICROSCOPYf_plane_restr0.0032455
ELECTRON MICROSCOPYf_dihedral_angle_d8.52525425
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.41840737371E-11
ens_1d_3CCELECTRON MICROSCOPYNCS constraints7.65436965347E-11
ens_1d_4CCELECTRON MICROSCOPYNCS constraints4.08236955928E-12
ens_1d_5CCELECTRON MICROSCOPYNCS constraints1.85551722166E-11
ens_2d_2NeELECTRON MICROSCOPYNCS constraints9.55039733001E-14
ens_2d_3NeELECTRON MICROSCOPYNCS constraints1.06638514424E-12
ens_2d_4NeELECTRON MICROSCOPYNCS constraints5.54857930813E-12
ens_2d_5NeELECTRON MICROSCOPYNCS constraints1.99663422443E-10

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