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Yorodumi- EMDB-14073: Cryo-EM structure of human full-length beta3gamma2 GABA(A)R in co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14073 | ||||||||||||||||||
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Title | Cryo-EM structure of human full-length beta3gamma2 GABA(A)R in complex with GABA and nanobody Nb25 | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | pentameric ligand-gated ion channel / neurotransmitter receptor / GABA receptor / MEMBRANE PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / chloride transport ...cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / chloride transport / neurotransmitter receptor activity / chloride channel activity / roof of mouth development / Signaling by ERBB4 / chloride channel complex / transmembrane transporter complex / extracellular ligand-gated monoatomic ion channel activity / chloride transmembrane transport / cytoplasmic vesicle membrane / postsynaptic membrane / neuron projection / synapse / signal transduction / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Sente A / Desai R | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: Nature / Year: 2022 Title: Differential assembly diversifies GABA receptor structures and signalling. Authors: Andrija Sente / Rooma Desai / Katerina Naydenova / Tomas Malinauskas / Youssef Jounaidi / Jonas Miehling / Xiaojuan Zhou / Simonas Masiulis / Steven W Hardwick / Dimitri Y Chirgadze / Keith ...Authors: Andrija Sente / Rooma Desai / Katerina Naydenova / Tomas Malinauskas / Youssef Jounaidi / Jonas Miehling / Xiaojuan Zhou / Simonas Masiulis / Steven W Hardwick / Dimitri Y Chirgadze / Keith W Miller / A Radu Aricescu / Abstract: Type A γ-aminobutyric acid receptors (GABARs) are pentameric ligand-gated chloride channels that mediate fast inhibitory signalling in neural circuits and can be modulated by essential medicines ...Type A γ-aminobutyric acid receptors (GABARs) are pentameric ligand-gated chloride channels that mediate fast inhibitory signalling in neural circuits and can be modulated by essential medicines including general anaesthetics and benzodiazepines. Human GABAR subunits are encoded by 19 paralogous genes that can, in theory, give rise to 495,235 receptor types. However, the principles that govern the formation of pentamers, the permutational landscape of receptors that may emerge from a subunit set and the effect that this has on GABAergic signalling remain largely unknown. Here we use cryogenic electron microscopy to determine the structures of extrasynaptic GABARs assembled from α4, β3 and δ subunits, and their counterparts incorporating γ2 instead of δ subunits. In each case, we identified two receptor subtypes with distinct stoichiometries and arrangements, all four differing from those previously observed for synaptic, α1-containing receptors. This, in turn, affects receptor responses to physiological and synthetic modulators by creating or eliminating ligand-binding sites at subunit interfaces. We provide structural and functional evidence that selected GABAR arrangements can act as coincidence detectors, simultaneously responding to two neurotransmitters: GABA and histamine. Using assembly simulations and single-cell RNA sequencing data, we calculated the upper bounds for receptor diversity in recombinant systems and in vivo. We propose that differential assembly is a pervasive mechanism for regulating the physiology and pharmacology of GABARs. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14073.map.gz | 71.7 MB | EMDB map data format | |
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Header (meta data) | emd-14073-v30.xml emd-14073.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14073_fsc.xml | 8.7 KB | Display | FSC data file |
Images | emd_14073.png | 57.6 KB | ||
Filedesc metadata | emd-14073.cif.gz | 6.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14073 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14073 | HTTPS FTP |
-Validation report
Summary document | emd_14073_validation.pdf.gz | 532.4 KB | Display | EMDB validaton report |
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Full document | emd_14073_full_validation.pdf.gz | 532 KB | Display | |
Data in XML | emd_14073_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_14073_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14073 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14073 | HTTPS FTP |
-Related structure data
Related structure data | 7qnbMC 7qn5C 7qn6C 7qn7C 7qn8C 7qn9C 7qnaC 7qncC 7qndC 7qneC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-10909 (Title: Cryo-EM micrographs of GABA(A)Rs purified from cells expressing human full-length alpha4, beta3 and gamma2 subunits, in presence of GABA and nanobody Nb25 Data size: 3.8 TB Data #1: Unaligned multi-frame micrographs of GABA(A) receptors purified from cells expressing alpha4, beta3 and gamma2 subunits [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14073.map.gz / Format: CCP4 / Size: 93 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: 0.896 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Human full-length beta3gamma2 GABA(A)R in complex with GABA and N...
Entire | Name: Human full-length beta3gamma2 GABA(A)R in complex with GABA and Nanobody Nb25 |
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Components |
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-Supramolecule #1: Human full-length beta3gamma2 GABA(A)R in complex with GABA and N...
Supramolecule | Name: Human full-length beta3gamma2 GABA(A)R in complex with GABA and Nanobody Nb25 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Gamma-aminobutyric acid type A receptor subunit gamma2
Macromolecule | Name: Gamma-aminobutyric acid type A receptor subunit gamma2 type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.666809 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GQKSDDDYED YTSNKTWVLT PKVPEGDVTV ILNNLLEGYD NKLRPDIGVK PTLIHTDMY VNSIGPVNAI NMEYTIDIFF AQTWYDRRLK FNSTIKVLRL NSNMVGKIWI PDTFFRNSKK ADAHWITTPN R MLRIWNDG ...String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GQKSDDDYED YTSNKTWVLT PKVPEGDVTV ILNNLLEGYD NKLRPDIGVK PTLIHTDMY VNSIGPVNAI NMEYTIDIFF AQTWYDRRLK FNSTIKVLRL NSNMVGKIWI PDTFFRNSKK ADAHWITTPN R MLRIWNDG RVLYTLRLTI DAECQLQLHN FPMDEHSCPL EFSSYGYPRE EIVYQWKRSS VEVGDTRSWR LYQFSFVGLR NT TEVVKTT SGDYVVMSVY FDLSRRMGYF TIQTYIPCTL IVVLSWVSFW INKDAVPART SLGITTVLTM TTLSTIARKS LPK VSYVTA MDLFVSVCFI FVFSALVEYG TLHYFVSNRK PSKDKDKKKK NPLLRMFSFK APTIDIRPRS ATIQMNNATH LQER DEEYG YECLDGKDCA SFFCCFEDCR TGAWRHGRIH IRIAKMDSYA RIFFPTAFCL FNLVYWVSYL YLGTGGSGGS GGSTE TSQV APA UniProtKB: Gamma-aminobutyric acid type A receptor subunit gamma2 |
-Macromolecule #2: Gamma-aminobutyric acid receptor subunit beta-3
Macromolecule | Name: Gamma-aminobutyric acid receptor subunit beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.180348 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 VNYIFFGRGP QRQKKLAEKT AKAKNDRSKS ESNRVDAHGN ILLTSLEVHN EMNEVSGGIG DTRNSAISFD NSGI QYRKQ SMPREGHGRF LGDRSLPHKK THLRRRSSQL KIKIPDLTDV NAIDRWSRIV FPFTFSLFNL VYWLYYVN UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3 |
-Macromolecule #3: Nanobody Nb25
Macromolecule | Name: Nanobody Nb25 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 13.341741 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLVESGGG LVQGSLRLSC AASGHTFNYP IMGWFRQAPG KEREFVGAIS WSGGSTSYAD SVKDRFTISR DNAKNTVYLE MNNLKPEDT AVYYCAAKGR YSGGLYYPTN YDYWGQGTQV TV |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #7: GAMMA-AMINO-BUTANOIC ACID
Macromolecule | Name: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 7 / 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: 7.6 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 287 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.46 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7qnb: |