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Yorodumi- EMDB-6998: Cryo-EM structure of the human alpha5beta3 GABAA receptor in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6998 | ||||||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of the human alpha5beta3 GABAA receptor in complex with GABA and Nb25 | ||||||||||||||||||||||||||||||||||||||||||
Map data | CryoEM Structure of the human %u03B15%u03B23 GABAA receptor | ||||||||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | IRON CHANNEL / MEMBRANE PROTEIN | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information inner ear receptor cell development / cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / GABA receptor binding / inhibitory synapse assembly / innervation / synaptic transmission, GABAergic ...inner ear receptor cell development / cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / GABA receptor binding / inhibitory synapse assembly / innervation / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / neurotransmitter receptor activity / cochlea development / roof of mouth development / neuronal cell body membrane / Signaling by ERBB4 / associative learning / chloride channel complex / regulation of postsynaptic membrane potential / transmembrane transporter complex / behavioral fear response / GABA-ergic synapse / chloride transmembrane transport / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / signaling receptor activity / presynaptic membrane / postsynapse / neuron projection / synapse / signal transduction / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | ||||||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.51 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Liu S / Xu L | ||||||||||||||||||||||||||||||||||||||||||
Funding support | China, United States, 13 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6998.map.gz | 27.5 MB | EMDB map data format | |
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Header (meta data) | emd-6998-v30.xml emd-6998.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6998_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_6998.png | 144.4 KB | ||
Filedesc metadata | emd-6998.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6998 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6998 | HTTPS FTP |
-Validation report
Summary document | emd_6998_validation.pdf.gz | 453.6 KB | Display | EMDB validaton report |
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Full document | emd_6998_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | emd_6998_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | emd_6998_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6998 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6998 | HTTPS FTP |
-Related structure data
Related structure data | 6a96MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6998.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM Structure of the human %u03B15%u03B23 GABAA receptor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pentameric complex of 1 alpha and 4 beta GABA receptor
Entire | Name: Pentameric complex of 1 alpha and 4 beta GABA receptor |
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Components |
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-Supramolecule #1: Pentameric complex of 1 alpha and 4 beta GABA receptor
Supramolecule | Name: Pentameric complex of 1 alpha and 4 beta GABA receptor type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Nb25
Macromolecule | Name: Nb25 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 13.673024 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLQESGGG LVQAGGSLRL SCAASGHTFN YPIMGWFRQA PGKEREFVGA ISWSGGSTSY ADSVKDRFTI SRDNAKNTVY LEMNNLKPE DTAVYYCAAK GRYSGGLYYP TNYDYWGQGT QVTVSS |
-Macromolecule #2: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyri...
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.052711 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyr...
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.456113 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #8: GAMMA-AMINO-BUTANOIC ACID
Macromolecule | Name: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 8 / Number of copies: 1 / Formula: ABU |
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Molecular weight | Theoretical: 103.12 Da |
Chemical component information | ChemComp-ABU: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |