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- EMDB-6998: Cryo-EM structure of the human alpha5beta3 GABAA receptor in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-6998
TitleCryo-EM structure of the human alpha5beta3 GABAA receptor in complex with GABA and Nb25
Map dataCryoEM Structure of the human %u03B15%u03B23 GABAA receptor
Sample
  • Complex: Pentameric complex of 1 alpha and 4 beta GABA receptor
    • Protein or peptide: Nb25
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
KeywordsIRON CHANNEL / MEMBRANE PROTEIN
Function / homology
Function and homology information


inner ear receptor cell development / GABA receptor binding / innervation / cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / neuronal cell body membrane ...inner ear receptor cell development / GABA receptor binding / innervation / cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / neuronal cell body membrane / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / synaptic transmission, GABAergic / cochlea development / associative learning / roof of mouth development / Signaling by ERBB4 / chloride channel complex / behavioral fear response / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / cytoplasmic vesicle membrane / chloride transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / signaling receptor activity / presynaptic membrane / dendritic spine / postsynaptic membrane / postsynapse / signal transduction / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, alpha subunit / Gamma-aminobutyric-acid A receptor, beta subunit / : / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, alpha subunit / Gamma-aminobutyric-acid A receptor, beta subunit / : / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 / Gamma-aminobutyric acid receptor subunit alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsLiu S / Xu L
Funding support China, United States, 13 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500404 China
Ministry of Science and Technology (China)2014CB910300 China
Ministry of Science and Technology (China)2016YFA0501102 China
National Natural Science Foundation of China31630030 China
National Natural Science Foundation of China31525001 China
National Natural Science Foundation of China31430019 China
National Natural Science Foundation of China31600606 China
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM071940 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10RR23057 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD018111 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)U24GM116792 United States
National Science Foundation (China)DBI-1338135 China
National Science Foundation (China)DMR-1548924 China
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 /
History
DepositionJul 11, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseOct 3, 2018-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6a96
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6998.png

Downloads & links

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Map

FileDownload / File: emd_6998.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM Structure of the human %u03B15%u03B23 GABAA receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-12.891079 - 22.949110000000001
Average (Standard dev.)-0.023008518 (±0.8374582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-12.89122.949-0.023

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Supplemental data

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Sample components

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Entire : Pentameric complex of 1 alpha and 4 beta GABA receptor

EntireName: Pentameric complex of 1 alpha and 4 beta GABA receptor
Components
  • Complex: Pentameric complex of 1 alpha and 4 beta GABA receptor
    • Protein or peptide: Nb25
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
  • Ligand: GAMMA-AMINO-BUTANOIC ACID

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Supramolecule #1: Pentameric complex of 1 alpha and 4 beta GABA receptor

SupramoleculeName: Pentameric complex of 1 alpha and 4 beta GABA receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nb25

MacromoleculeName: Nb25 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.673024 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGHTFN YPIMGWFRQA PGKEREFVGA ISWSGGSTSY ADSVKDRFTI SRDNAKNTVY LEMNNLKPE DTAVYYCAAK GRYSGGLYYP TNYDYWGQGT QVTVSS

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Macromolecule #2: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyri...

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.052711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWGLAGGRLF GIFSAPVLVA VVCCAQSVND PGNMSFVKET VDKLLKGYDI RLRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQ QYWRDKRLAY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY ...String:
MWGLAGGRLF GIFSAPVLVA VVCCAQSVND PGNMSFVKET VDKLLKGYDI RLRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQ QYWRDKRLAY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY PLDEQNCTLE IESYGYTTDD IEFYWRGGDK AVTGVERIEL PQFSIVEHRL VSRNVVFATG AYPRLSLSFR LK RNIGYFI LQTYMPSILI TILSWVSFWI NYDASAARVA LGITTVLTMT TINTHLRETL PKIPYVKAID MYLMGCFVFV FLA LLEYAF VNYIFFSQPA RAAAIDRWSR IVFPFTFSLF NLVYWLYYVN

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3, Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #3: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyr...

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.456113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDNGMFSGFI MIKNLLLFCI SMNLSSHFGF SQMPTSSVKD ETNDNITIFT RILDGLLDGY DNRLRPGLGE RITQVRTDIY VTSFGPVSD TEMEYTIDVF FRQSWKDERL RFKGPMQRLP LNNLLASKIW TPDTFFHNGK KSIAHNMTTP NKLLRLEDDG T LLYTMRLT ...String:
MDNGMFSGFI MIKNLLLFCI SMNLSSHFGF SQMPTSSVKD ETNDNITIFT RILDGLLDGY DNRLRPGLGE RITQVRTDIY VTSFGPVSD TEMEYTIDVF FRQSWKDERL RFKGPMQRLP LNNLLASKIW TPDTFFHNGK KSIAHNMTTP NKLLRLEDDG T LLYTMRLT ISAECPMQLE DFPMDAHACP LKFGSYAYPN SEVVYVWTNG STKSVVVAED GSRLNQYHLM GQTVGTENIS TS TGEYTIM TAHFHLKRKI GYFVIQTYLP CIMTVILSQV SFWLNRESVP ARTVFGVTTV LTMTTLSISA RNSLPKVAYA TAM DWFIAV CYAFVFSALI EFATVNYFTK SQPARAAKID KMSRIVFPVL FGTFNLVYWA TYLNREPVIK GAASPK

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-5, Gamma-aminobutyric acid receptor subunit alpha-5

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Macromolecule #8: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 8 / Number of copies: 1 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 8.0 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.55) / Number images used: 161455
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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