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- EMDB-0275: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0275 | |||||||||||||||||||||||||||
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Title | CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. | |||||||||||||||||||||||||||
![]() | Synaptic human full-length a1b3g2L GABAAR in complex with picrotoxin and megabody Mb38. Sharpened and filtered map (Relion post-processing). | |||||||||||||||||||||||||||
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Function / homology | ![]() GABA receptor activation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() | |||||||||||||||||||||||||||
![]() | Masiulis S / Desai R / Uchanski T / Serna Martin I / Laverty D / Karia D / Malinauskas T / Jasenko Z / Pardon E / Kotecha A ...Masiulis S / Desai R / Uchanski T / Serna Martin I / Laverty D / Karia D / Malinauskas T / Jasenko Z / Pardon E / Kotecha A / Steyaert J / Miller KW / Aricescu AR | |||||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: GABA receptor signalling mechanisms revealed by structural pharmacology. Authors: Simonas Masiulis / Rooma Desai / Tomasz Uchański / Itziar Serna Martin / Duncan Laverty / Dimple Karia / Tomas Malinauskas / Jasenko Zivanov / Els Pardon / Abhay Kotecha / Jan Steyaert / ...Authors: Simonas Masiulis / Rooma Desai / Tomasz Uchański / Itziar Serna Martin / Duncan Laverty / Dimple Karia / Tomas Malinauskas / Jasenko Zivanov / Els Pardon / Abhay Kotecha / Jan Steyaert / Keith W Miller / A Radu Aricescu / ![]() ![]() ![]() ![]() Abstract: Type-A γ-aminobutyric (GABA) receptors are ligand-gated chloride channels with a very rich pharmacology. Some of their modulators, including benzodiazepines and general anaesthetics, are among the ...Type-A γ-aminobutyric (GABA) receptors are ligand-gated chloride channels with a very rich pharmacology. Some of their modulators, including benzodiazepines and general anaesthetics, are among the most successful drugs in clinical use and are common substances of abuse. Without reliable structural data, the mechanistic basis for the pharmacological modulation of GABA receptors remains largely unknown. Here we report several high-resolution cryo-electron microscopy structures in which the full-length human α1β3γ2L GABA receptor in lipid nanodiscs is bound to the channel-blocker picrotoxin, the competitive antagonist bicuculline, the agonist GABA (γ-aminobutyric acid), and the classical benzodiazepines alprazolam and diazepam. We describe the binding modes and mechanistic effects of these ligands, the closed and desensitized states of the GABA receptor gating cycle, and the basis for allosteric coupling between the extracellular, agonist-binding region and the transmembrane, pore-forming region. This work provides a structural framework in which to integrate previous physiology and pharmacology research and a rational basis for the development of GABA receptor modulators. | |||||||||||||||||||||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.7 KB 29.7 KB | Display Display | ![]() |
Images | ![]() | 190.9 KB | ||
Others | ![]() ![]() ![]() | 49.7 MB 49.8 MB 49.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hugMC ![]() 0279C ![]() 0280C ![]() 0282C ![]() 0283C ![]() 6hujC ![]() 6hukC ![]() 6huoC ![]() 6hupC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Synaptic human full-length a1b3g2L GABAAR in complex with picrotoxin and megabody Mb38. Sharpened and filtered map (Relion post-processing). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_0275_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: Half-map 2
File | emd_0275_half_map_1.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
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Density Histograms |
-Half map: Half-map 1
File | emd_0275_half_map_2.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Human full-length heteromeric alpha1beta3gamma2L GABA(A)R in comp...
Entire | Name: Human full-length heteromeric alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. |
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Components |
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-Supramolecule #1: Human full-length heteromeric alpha1beta3gamma2L GABA(A)R in comp...
Supramolecule | Name: Human full-length heteromeric alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 330 KDa |
-Supramolecule #2: Human full-length heteromeric alpha1beta3gamma2L GABA(A)R in comp...
Supramolecule | Name: Human full-length heteromeric alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: Human full-length heteromeric alpha1beta3gamma2L GABA(A)R in comp...
Supramolecule | Name: Human full-length heteromeric alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38. type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Gamma-aminobutyric acid receptor subunit alpha-1
Macromolecule | Name: Gamma-aminobutyric acid receptor subunit alpha-1 / type: protein_or_peptide / ID: 1 Details: Potential signal peptide: MKKSPGLSDY LWAWTLFLST LTGRSYG FLAG tag: DYKDDDDK Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 49.85209 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DYKDDDDKQP SLQDELKDNT TVFTRILDRL LDGYDNRLRP GLGERVTEVK TDIFVTSFGP VSDHDMEYTI DVFFRQSWKD ERLKFKGPM TVLRLNNLMA SKIWTPDTFF HNGKKSVAHN MTMPNKLLRI TEDGTLLYTM RLTVRAECPM HLEDFPMDAH A CPLKFGSY ...String: DYKDDDDKQP SLQDELKDNT TVFTRILDRL LDGYDNRLRP GLGERVTEVK TDIFVTSFGP VSDHDMEYTI DVFFRQSWKD ERLKFKGPM TVLRLNNLMA SKIWTPDTFF HNGKKSVAHN MTMPNKLLRI TEDGTLLYTM RLTVRAECPM HLEDFPMDAH A CPLKFGSY AYTRAEVVYE WTREPARSVV VAEDGSRLNQ YDLLGQTVDS GIVQSSTGEY VVMTTHFHLK RKIGYFVIQT YL PCIMTVI LSQVSFWLNR ESVPARTVFG VTTVLTMTTL SISARNSLPK VAYATAMDWF IAVCYAFVFS ALIEFATVNY FTK RGYAWD GKSVVPEKPK KVKDPLIKKN NTYAPTATSY TPNLARGDPG LATIAKSATI EPKEVKPETK PPEPKKTFNS VSKI DRLSR IAFPLLFGIF NLVYWATYLN REPQLKAPTP HQ |
-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: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 54.444578 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MCSGLLELLL PIWLSWTLGT RGSEPRSVND PGNMSFVKET VDKLLKGYDI RLRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQ QYWRDKRLAY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY ...String: MCSGLLELLL PIWLSWTLGT RGSEPRSVND 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 |
-Macromolecule #3: Gamma-aminobutyric acid receptor subunit gamma-2
Macromolecule | Name: Gamma-aminobutyric acid receptor subunit gamma-2 / type: protein_or_peptide / ID: 3 / Details: Linker sequence: GGSGGSGGSGK 1D4 tag: TETSQVAPA / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 56.922055 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSSPNIWSTG SSVYSTPVFS QKMTVWILLL LSLYPGFTSQ KSDDDYEDYA SNKTWVLTPK VPEGDVTVIL NNLLEGYDNK LRPDIGVKP TLIHTDMYVN SIGPVNAINM EYTIDIFFAQ TWYDRRLKFN STIKVLRLNS NMVGKIWIPD TFFRNSKKAD A HWITTPNR ...String: MSSPNIWSTG SSVYSTPVFS QKMTVWILLL LSLYPGFTSQ KSDDDYEDYA SNKTWVLTPK VPEGDVTVIL NNLLEGYDNK LRPDIGVKP TLIHTDMYVN SIGPVNAINM EYTIDIFFAQ TWYDRRLKFN STIKVLRLNS NMVGKIWIPD TFFRNSKKAD A HWITTPNR MLRIWNDGRV LYTLRLTIDA ECQLQLHNFP MDEHSCPLEF SSYGYPREEI VYQWKRSSVE VGDTRSWRLY QF SFVGLRN TTEVVKTTSG DYVVMSVYFD LSRRMGYFTI QTYIPCTLIV VLSWVSFWIN KDAVPARTSL GITTVLTMTT LST IARKSL PKVSYVTAMD LFVSVCFIFV FSALVEYGTL HYFVSNRKPS KDKDKKKKNP LLRMFSFKAP TIDIRPRSAT IQMN NATHL QERDEEYGYE CLDGKDCASF FCCFEDCRTG AWRHGRIHIR IAKMDSYARI FFPTAFCLFN LVYWVSYLYL GGSGG SGGS GKTETSQVAP A |
-Macromolecule #4: Megabody Mb38
Macromolecule | Name: Megabody Mb38 / type: protein_or_peptide / ID: 4 / Details: 6His tag: HHHHHH EPEA tag: EPEA / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 57.784301 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: QVQLQESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK ...String: QVQLQESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK CDASAISSAN MTMQNQKNNW GNGCAGVEET QSLLKTSAAD FNNQTPQINQ AQNLANTLIQ ELGNNPFRAS GG GSGGGGS GKLSDTYEQL SRLLTNDNGT NSKTSAQAIN QAVNNLNERA KTLAGGTTNS PAYQATLLAL RSVLGLWNSM GYA VICGGY TKSPGENNQK DFHYTDENGN GTTINCGGST NSNGTHSYNG TNTLKADKNV SLSIEQYEKI HEAYQILSKA LKQA GLAPL NSKGEKLEAH VTTSKYGSLR VSCAASGRTF TTYIMAWFRQ APGKEREFLA AMDQGRIQYY GDSVRGRFTI SRDYA KNSV DLQLDGLRPE DTAVYYCAAG AGFWGLRTAS SYHYWGQGTQ VTVSSHHHHH HEPEA |
-Macromolecule #9: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...
Macromolecule | Name: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate type: ligand / ID: 9 / Number of copies: 2 / Formula: PIO |
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Molecular weight | Theoretical: 746.566 Da |
Chemical component information | ![]() ChemComp-PIO: |
-Macromolecule #10: (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-...
Macromolecule | Name: (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione type: ligand / ID: 10 / Number of copies: 1 / Formula: RI5 |
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Molecular weight | Theoretical: 292.284 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE Details: 3.5 ul of 0.1 mg/ml protein solution was applied on a grid in the Vitrobot MkIV chamber set to 95% RH at 14.5 degC for 30s and then blotted for 5.5 s and plunged |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
Details | Monodisperse sample |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: Gctf (ver. 1.08) |
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Startup model | Type of model: OTHER / Details: Relion 3D ab-initio |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0) / Software - details: Refine3D |
Final 3D classification | Software - Name: RELION (ver. 3.0) / Software - details: Class3D |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0) / Software - details: Refine3D |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Software - details: Refine3D / Number images used: 56269 |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6hug: |