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Yorodumi- EMDB-9403: Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9403 | |||||||||
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Title | Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, Glycine bound, desensitized state | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / synaptic transmission, glycinergic / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / glycinergic synapse ...glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / synaptic transmission, glycinergic / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / glycinergic synapse / adult walking behavior / neurotransmitter receptor activity / glycine binding / startle response / neuropeptide signaling pathway / transmembrane transporter complex / GABA-ergic synapse / monoatomic ion transport / chloride transmembrane transport / visual perception / bioluminescence / generation of precursor metabolites and energy / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / nervous system development / chemical synaptic transmission / postsynaptic membrane / neuron projection / dendrite / synapse / protein-containing complex binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Yu H / Wang W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Neuron / Year: 2021 Title: Characterization of the subunit composition and structure of adult human glycine receptors. Authors: Hailong Yu / Xiao-Chen Bai / Weiwei Wang / Abstract: The strychnine-sensitive pentameric glycine receptor (GlyR) mediates fast inhibitory neurotransmission in the mammalian nervous system. Only heteromeric GlyRs mediate synaptic transmission, as they ...The strychnine-sensitive pentameric glycine receptor (GlyR) mediates fast inhibitory neurotransmission in the mammalian nervous system. Only heteromeric GlyRs mediate synaptic transmission, as they contain the β subunit that permits clustering at the synapse through its interaction with scaffolding proteins. Here, we show that α2 and β subunits assemble with an unexpected 4:1 stoichiometry to produce GlyR with native electrophysiological properties. We determined structures in multiple functional states at 3.6-3.8 Å resolutions and show how 4:1 stoichiometry is consistent with the structural features of α2β GlyR. Furthermore, we show that one single β subunit in each GlyR gives rise to the characteristic electrophysiological properties of heteromeric GlyR, while more β subunits render GlyR non-conductive. A single β subunit ensures a univalent GlyR-scaffold linkage, which means the scaffold alone regulates the cluster properties. | |||||||||
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_9403.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-9403-v30.xml emd-9403.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_9403.png | 161.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9403 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9403 | HTTPS FTP |
-Validation report
Summary document | emd_9403_validation.pdf.gz | 473.1 KB | Display | EMDB validaton report |
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Full document | emd_9403_full_validation.pdf.gz | 472.7 KB | Display | |
Data in XML | emd_9403_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_9403_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9403 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9403 | HTTPS FTP |
-Related structure data
Related structure data | 5bkfMC 9404C 5bkgC 7kuyC 7l31C 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_9403.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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 : Glycine receptor alpha2-beta heteromer, glycine bound, desensitiz...
Entire | Name: Glycine receptor alpha2-beta heteromer, glycine bound, desensitized state |
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Components |
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-Supramolecule #1: Glycine receptor alpha2-beta heteromer, glycine bound, desensitiz...
Supramolecule | Name: Glycine receptor alpha2-beta heteromer, glycine bound, desensitized state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Experimental: 257 KDa |
-Supramolecule #2: Glycine receptor alpha2
Supramolecule | Name: Glycine receptor alpha2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: Glycine receptor beta, GFP chimera
Supramolecule | Name: Glycine receptor beta, GFP chimera / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Glycine receptor subunit alpha-2
Macromolecule | Name: Glycine receptor subunit alpha-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.676004 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KDHDSRSGKQ PSQTLSPSDF LDKLMGRTSG YDARIRPNFK GPPVNVTCNI FINSFGSVTE TTMDYRVNIF LRQQWNDSRL AYSEYPDDS LDLDPSMLDS IWKPDLFFAN EKGANFHDVT TDNKLLRISK NGKVLYSIRL TLTLSCPMDL KNFPMDVQTC T MQLESFGY ...String: KDHDSRSGKQ PSQTLSPSDF LDKLMGRTSG YDARIRPNFK GPPVNVTCNI FINSFGSVTE TTMDYRVNIF LRQQWNDSRL AYSEYPDDS LDLDPSMLDS IWKPDLFFAN EKGANFHDVT TDNKLLRISK NGKVLYSIRL TLTLSCPMDL KNFPMDVQTC T MQLESFGY TMNDLIFEWL SDGPVQVAEG LTLPQFILKE EKELGYCTKH YNTGKFTCIE VKFHLERQMG YYLIQMYIPS LL IVILSWV SFWINMDAAP ARVALGITTV LTMTTQSSGS RASLPKVSYV KAIDIWMAVC LLFVFAALLE YAAVNFVSRG SSG KKFVDR AKRIDTISRA AFPLAFLIFN IFYWITYKII RHEDVHKK |
-Macromolecule #2: Glycine receptor subunit beta,Green fluorescent protein
Macromolecule | Name: Glycine receptor subunit beta,Green fluorescent protein type: protein_or_peptide / ID: 2 Details: This is a GFP insertion between helices M3-M4 of Glycine Receptor Beta Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 78.765086 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GVAMPGAEDD VVAALEVLFQ GPKSSKKGKG KKKQYLCPSQ QSAEDLARVP ANSTSNILNR LLVSYDPRIR PNFKGIPVDV VVNIFINSF GSIQETTMDY RVNIFLRQKW NDPRLKLPSD FRGSDALTVD PTMYKCLWKP DLFFANEKSA NFHDVTQENI L LFIFRDGD ...String: GVAMPGAEDD VVAALEVLFQ GPKSSKKGKG KKKQYLCPSQ QSAEDLARVP ANSTSNILNR LLVSYDPRIR PNFKGIPVDV VVNIFINSF GSIQETTMDY RVNIFLRQKW NDPRLKLPSD FRGSDALTVD PTMYKCLWKP DLFFANEKSA NFHDVTQENI L LFIFRDGD VLVSMRLSIT LSCPLDLTLF PMDTQRCKMQ LESFGYTTDD LRFIWQSGDP VQLEKIALPQ FDIKKEDIEY GN CTKYYKG TGYYTCVEVI FTLRRQVGFY MMGVYAPTLL IVVLSWLSFW INPDASAARV PLGIFSVLSL ASECTTLAAE LPK VSYVKA LDVWLIACLL FGFASLVEYA VVQVMLNGGS SAAAVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYG KLTLK FICTTGKLPV PWPTLVTTLT YGVQCFSRYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRAEVKFE GDTLV NRIE LKGIDFKEDG NILGHKLEYN YNSHNVYIMA DKQKNGIKVN FKIRHNIEDG SVQLADHYQQ NTPIGDGPVL LPDNHY LST QSKLSKDPNE KRDHMVLLEF VTAAGITLGM DELYKSGSGS GVGETRCKKV CTSKSDLRSN DFSIVGSLPR DFELSNY DC YGKPIEVNNG LGKSQAKNNK KPPPAKPVIP TAAKRIDLYA RALFPFCFLF FNVIYWSIYL |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: GLYCINE
Macromolecule | Name: GLYCINE / type: ligand / ID: 4 / Number of copies: 5 / Formula: GLY |
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Molecular weight | Theoretical: 75.067 Da |
Chemical component information | ChemComp-GLY: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.0 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5999 / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.2 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |