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- EMDB-50367: Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50367
TitleCryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived asymmetric bound-closed 1 state of branch 1
Map dataUnsharpened map
Sample
  • Complex: Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived asymmetric pre-active 1 state of branch 1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Megabody25,Outer membrane protein
  • Ligand: DECANE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHLORIDE ION
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
KeywordsGABA / neurotransmission / gating cycle / time-resolved cryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


circadian sleep/wake cycle, REM sleep / reproductive behavior / GABA receptor complex / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity ...circadian sleep/wake cycle, REM sleep / reproductive behavior / GABA receptor complex / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / innervation / response to anesthetic / postsynaptic specialization membrane / inhibitory postsynaptic potential / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / cellular response to zinc ion / exploration behavior / motor behavior / roof of mouth development / Signaling by ERBB4 / cochlea development / social behavior / chloride channel complex / dendrite membrane / cytoplasmic vesicle membrane / chloride transmembrane transport / cerebellum development / learning / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / memory / dendritic spine / postsynaptic membrane / postsynapse / response to xenobiotic stimulus / cell surface / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : / Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha ...SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Gamma-aminobutyric-acid A receptor, alpha 1 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, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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
Outer membrane protein / Gamma-aminobutyric acid receptor subunit alpha-1 / Gamma-aminobutyric acid receptor subunit beta-3
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMihaylov DB / Malinauskas T / Aricescu AR
Funding support United Kingdom, United States, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
Cancer Research UKDRCRPG-May23/100002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_EX_MR/T046279/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01-GM135550 United States
National Science Foundation (NSF, United States)NeuroNex 2014862 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 23, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50367.png

Downloads & links

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Map

FileDownload / File: emd_50367.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 210 pix.
= 260.383 Å		1.24 Å/pix.
x 210 pix.
= 260.383 Å		1.24 Å/pix.
x 210 pix.
= 260.383 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23992 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5730649 - 1.9054174
Average (Standard dev.)0.0064330525 (±0.08340934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 260.3832 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50367_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_50367_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the half maps

Fileemd_50367_half_map_1.map
AnnotationOne of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the half maps

Fileemd_50367_half_map_2.map
AnnotationOne of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex ...

EntireName: Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived asymmetric pre-active 1 state of branch 1
Components
  • Complex: Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived asymmetric pre-active 1 state of branch 1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Megabody25,Outer membrane protein
  • Ligand: DECANE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHLORIDE ION
  • Ligand: GAMMA-AMINO-BUTANOIC ACID

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Supramolecule #1: Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex ...

SupramoleculeName: Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived asymmetric pre-active 1 state of branch 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Gamma-aminobutyric acid receptor subunit alpha-1

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.059648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPDY DIPTTENLYF QGTGQPSQDE LKDNTTVFTR ILDRLLDGYD NRLRPGLGE RVTEVKTDIF VTSFGPVSDH DMEYTIDVFF RQSWKDERLK FKGPMTVLRL NNLMASKIWT PDTFFHNGKK S VAHNMTMP ...String:
MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPDY DIPTTENLYF QGTGQPSQDE LKDNTTVFTR ILDRLLDGYD NRLRPGLGE RVTEVKTDIF VTSFGPVSDH DMEYTIDVFF RQSWKDERLK FKGPMTVLRL NNLMASKIWT PDTFFHNGKK S VAHNMTMP NKLLRITEDG TLLYTMRLTV RAECPMHLED FPMDAHACPL KFGSYAYTRA EVVYEWTREP ARSVVVAEDG SR LNQYDLL GQTVDSGIVQ SSTGEYVVMT THFHLKRKIG YFVIQTYLPC IMTVILSQVS FWLNRESVPA RTVFGVTTVL TMT TLSISA RNSLPKVAYA TAMDWFIAVC YAFVFSALIE FATVNYFTKS QPARAAKIDR LSRIAFPLLF GIFNLVYWAT YLNR EPQLK APTPHQ

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-1, Gamma-aminobutyric acid receptor subunit alpha-1

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

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.643246 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPDY DIPTTENLYF QGTGQSVNDP GNMSFVKETV DKLLKGYDIR LRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQQ YWRDKRLAYS GIPLNLTLDN RVADQLWVPD TYFLNDKKSF V HGVTVKNR ...String:
MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPDY DIPTTENLYF QGTGQSVNDP GNMSFVKETV DKLLKGYDIR LRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQQ YWRDKRLAYS GIPLNLTLDN RVADQLWVPD TYFLNDKKSF V HGVTVKNR MIRLHPDGTV LYGLRITTTA ACMMDLRRYP LDEQNCTLEI ESYGYTTDDI EFYWRGGDKA VTGVERIELP QF SIVEHRL VSRNVVFATG AYPRLSLSFR LKRNIGYFIL QTYMPSILIT ILSWVSFWIN YDASAARVAL GITTVLTMTT INT HLRETL PKIPYVKAID MYLMGCFVFV FLALLEYAFV NYIFFSQPAR AAAIDRWSRI VFPFTFSLFN LVYWLYYVN

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

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Macromolecule #3: Megabody25,Outer membrane protein

MacromoleculeName: Megabody25,Outer membrane protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 56.300629 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVQLVESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK ...String:
QVQLVESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK CDASAISSAN MTMQNQKNNW GNGCAGVEET QSLLKTSAAD FNNQTPQINQ AQNLANTLIQ ELGNNTYEQL SR LLTNDNG TNSKTSAQAI NQAVNNLNER AKTLAGGTTN SPAYQATLLA LRSVLGLWNS MGYAVICGGY TKSPGENNQK DFH YTDENG NGTTINCGGS TNSNGTHSYN GTNTLKADKN VSLSIEQYEK IHEAYQILSK ALKQAGLAPL NSKGEKLEAH VTTS KYGSL RLSCAASGHT FNYPIMGWFR QAPGKEREFV GAISWSGGST SYADSVKDRF TISRDNAKNT VYLEMNNLKP EDTAV YYCA AKGRYSGGLY YPTNYDYWGQ GTQVTVSSHH HHHHEPEA

UniProtKB: Outer membrane protein, Outer membrane protein

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Macromolecule #6: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 6 / Number of copies: 3 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #7: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 7 / Number of copies: 2 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #8: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #9: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 9 / Number of copies: 2 / 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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
4.3 mMNa2HPODisodium phosphate

Details: 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: current: 30mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 18399 / Average exposure time: 4.34 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 96000
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

Particle selectionNumber selected: 9725751
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6huk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 30 / Target criteria: FSC at 0.5
Output model

PDB-9ffn:
Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived asymmetric bound-closed 1 state of branch 1

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