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- PDB-6a96: Cryo-EM structure of the human alpha5beta3 GABAA receptor in comp... -

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Basic information

Entry
Database: PDB / ID: 6a96
TitleCryo-EM structure of the human alpha5beta3 GABAA receptor in complex with GABA and Nb25
Components
  • (Gamma-aminobutyric acid receptor subunit ...) x 2
  • Nb25
KeywordsMEMBRANE PROTEIN / IRON CHANNEL
Function / homologyNeurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Gamma-aminobutyric-acid A receptor, alpha subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Gamma-aminobutyric-acid A receptor, beta subunit / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain ...Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Gamma-aminobutyric-acid A receptor, alpha subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Gamma-aminobutyric-acid A receptor, beta subunit / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channels signature. / Neurotransmitter receptors and postsynaptic signal transmission / GABA A receptor activation / Gamma-aminobutyric-acid A receptor, alpha 5 subunit / inner ear receptor cell development / GABA-gated chloride ion channel activity / GABA-A receptor activity / GABA-A receptor complex / cellular response to histamine / gamma-aminobutyric acid signaling pathway / GABA receptor binding / integral component of postsynaptic specialization membrane / innervation / GABA-ergic synapse / inhibitory postsynaptic potential / neuronal cell body membrane / chloride channel activity / chloride channel complex / chloride transmembrane transport / cochlea development / integral component of presynaptic membrane / roof of mouth development / extracellular ligand-gated ion channel activity / associative learning / behavioral fear response / transporter activity / sensory perception of sound / cytoplasmic vesicle membrane / brain development / chemical synaptic transmission / signaling receptor activity / postsynaptic membrane / negative regulation of neuron apoptotic process / cell junction / dendrite / integral component of plasma membrane / signal transduction / nucleoplasm / identical protein binding / plasma membrane / cytosol / Gamma-aminobutyric acid receptor subunit beta-3 / Gamma-aminobutyric acid receptor subunit alpha-5
Function and homology information
Specimen sourceLama glama (llama)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.51 Å resolution
AuthorsLiu, S. / Xu, L. / Guan, F. / Liu, Y.T. / Cui, Y. / Zhang, Q. / Bi, G.Q. / Zhou, Z.H. / Zhang, X. / Ye, S.
CitationJournal: Cell Res. / Year: 2018
Title: Cryo-EM structure of the human α5β3 GABA receptor.
Authors: Si Liu / Lingyi Xu / Fenghui Guan / Yun-Tao Liu / Yanxiang Cui / Qing Zhang / Xiang Zheng / Guo-Qiang Bi / Z Hong Zhou / Xiaokang Zhang / Sheng Ye
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 11, 2018 / Release: Oct 3, 2018

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Structure visualization

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  • EMDB-6998
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Assembly

Deposited unit
K: Nb25
L: Nb25
O: Nb25
B: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
A: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
E: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
C: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
D: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,35752
Polyers253,6868
Non-polymers8,67144
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)37350
ΔGint (kcal/M)-3
Surface area (Å2)98180

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Components

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Protein/peptide , 1 types, 3 molecules KLO

#1: Protein/peptide Nb25


Mass: 13673.024 Da / Num. of mol.: 3 / Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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

#2: Protein/peptide
Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3 / GABA(A) receptor subunit beta-3


Mass: 42052.711 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: GABRB3 / Production host: Homo sapiens (human) / References: UniProt: P28472
#3: Protein/peptide Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5 / GABA(A) receptor subunit alpha-5


Mass: 44456.113 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: GABRA5 / Production host: Homo sapiens (human) / References: UniProt: P31644

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Non-polymers , 4 types, 44 molecules

#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 20 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 9 / Formula: C6H12O6
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 14 / Formula: C6H12O6
#7: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Formula: C4H9NO2

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Pentameric complex of 1 alpha and 4 beta GABA receptor
Type: COMPLEX / Entity ID: 1,2,3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 70 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM softwareName: cryoSPARC / Version: 0.55 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 161455 / Algorithm: BACK PROJECTION / Symmetry type: POINT

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