[English] 日本語
Yorodumi
- PDB-9g2d: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g2d
TitleCryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state (C5) sprayed with PBS
ComponentsGamma-aminobutyric acid receptor subunit beta-3
KeywordsMEMBRANE PROTEIN / GABA / neurotransmission / gating cycle / time-resolved cryo-EM
Function / homology
Function and homology information


circadian sleep/wake cycle, REM sleep / reproductive behavior / 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 ...circadian sleep/wake cycle, REM sleep / reproductive behavior / 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 / 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 / response to xenobiotic stimulus / cell surface / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
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 ...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
Gamma-aminobutyric acid receptor subunit beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMihaylov, D.B. / Malinauskas, T. / Aricescu, A.R.
Funding support United Kingdom, United States, 6items
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: To Be Published
Title: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state (C5) sprayed with PBS
Authors: Mihaylov, D.B. / Malinauskas, T. / Aricescu, A.R.
History
DepositionJul 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor subunit beta-3
B: Gamma-aminobutyric acid receptor subunit beta-3
C: Gamma-aminobutyric acid receptor subunit beta-3
D: Gamma-aminobutyric acid receptor subunit beta-3
E: Gamma-aminobutyric acid receptor subunit beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,17625
Polymers228,2165
Non-polymers7,95920
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "E"
d_4ens_1chain "D"
d_5ens_1chain "A"
d_1ens_2chain "e"
d_2ens_2chain "b"
d_3ens_2chain "c"
d_4ens_2chain "d"
d_5ens_2chain "a"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNVALVALCC4 - 44758 - 394
d_21ens_1ASNASNVALVALBB4 - 44758 - 394
d_31ens_1ASNASNVALVALEE4 - 44758 - 394
d_41ens_1ASNASNVALVALDD4 - 44758 - 394
d_51ens_1ASNASNVALVALAA4 - 44758 - 394
d_11ens_2NAGNAGNAGNAGeN1
d_12ens_2NAGNAGNAGNAGeN2
d_13ens_2BMABMABMABMAeN3
d_14ens_2MANMANMANMANeN4
d_15ens_2MANMANMANMANeN5
d_16ens_2NAGNAGNAGNAGJO1
d_17ens_2NAGNAGNAGNAGJO2
d_18ens_2NAGNAGNAGNAGEY502
d_21ens_2NAGNAGNAGNAGbH1
d_22ens_2NAGNAGNAGNAGbH2
d_23ens_2BMABMABMABMAbH3
d_24ens_2MANMANMANMANbH4
d_25ens_2MANMANMANMANbH5
d_26ens_2NAGNAGNAGNAGGI1
d_27ens_2NAGNAGNAGNAGGI2
d_28ens_2NAGNAGNAGNAGBR501
d_31ens_2NAGNAGNAGNAGcJ1
d_32ens_2NAGNAGNAGNAGcJ2
d_33ens_2BMABMABMABMAcJ3
d_34ens_2MANMANMANMANcJ4
d_35ens_2MANMANMANMANcJ5
d_36ens_2NAGNAGNAGNAGHK1
d_37ens_2NAGNAGNAGNAGHK2
d_38ens_2NAGNAGNAGNAGCT501
d_41ens_2NAGNAGNAGNAGdL1
d_42ens_2NAGNAGNAGNAGdL2
d_43ens_2BMABMABMABMAdL3
d_44ens_2MANMANMANMANdL4
d_45ens_2MANMANMANMANdL5
d_46ens_2NAGNAGNAGNAGIM1
d_47ens_2NAGNAGNAGNAGIM2
d_48ens_2NAGNAGNAGNAGDW502
d_51ens_2NAGNAGNAGNAGaF1
d_52ens_2NAGNAGNAGNAGaF2
d_53ens_2BMABMABMABMAaF3
d_54ens_2MANMANMANMANaF4
d_55ens_2MANMANMANMANaF5
d_56ens_2NAGNAGNAGNAGFG1
d_57ens_2NAGNAGNAGNAGFG2
d_58ens_2NAGNAGNAGNAGAP501

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.309007401933, -0.951059623008, 0.000137967219673), (0.951059583662, 0.309007429381, 0.00027733073109), (-0.000306390956449, 4.55177978104E-5, 0.999999952026)296.295610848, -46.9823334307, 0.0573248284742
2given(-0.810226667398, 0.586116370736, -0.00058939988032), (-0.586116601282, -0.810226643284, 0.000340902363142), (-0.000277739030723, 0.000621665240246, 0.999999768197)221.036415466, 432.346404566, -0.041948580519
3given(0.308063165235, 0.951365796062, 0.000456407916257), (-0.951365836128, 0.308063290567, -0.000234207578273), (-0.000363419603671, -0.000362060170981, 0.999999868419)-46.8784685511, 296.607428949, 0.138199323012
4given(-0.808529559731, -0.588455558797, 7.97607021481E-5), (0.588455541747, -0.808529484006, 0.000385851085379), (-0.000162567336708, 0.000358907635376, 0.999999922379)432.534766967, 220.078120707, -0.0152446614557
5given(-0.808130917322, 0.589002875265, 0.000182751939624), (-0.589002869409, -0.808130937234, 9.00690637846E-5), (0.000200738433792, -3.48538216903E-5, 0.999999979245)220.012707074, 432.560723867, -0.0276476044033
6given(-0.809511473189, -0.587104057872, -2.47685494687E-6), (0.587104047911, -0.809511460217, 0.000180844532245), (-0.00010817960119, 0.00014494155215, 0.999999983645)432.502764939, 220.538847318, -0.00974298030573
7given(0.308504937075, -0.951222510102, 0.000663381211949), (0.951222739665, 0.30850490388, -0.00015435574885), (-5.78296941583E-5, 0.000678642804458, 0.99999976805)296.316607786, -46.8512351734, -0.110327401556
8given(0.309225408906, 0.950988743898, 0.000235510889194), (-0.950988772189, 0.309225409743, 3.3768940493E-5), (-4.07120689077E-5, -0.000234410425784, 0.999999971697)-46.9967524403, 296.269279375, 0.0434138594026

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Gamma-aminobutyric acid receptor subunit beta-3 / GABA(A) receptor subunit beta-3 / GABAAR subunit beta-3


Mass: 45643.246 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRB3 / Plasmid: pHLsec / Cell line (production host): EXPI 293F / Production host: Homo sapiens (human) / References: UniProt: P28472

-
Sugars , 3 types, 15 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 255 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state (C5) sprayed with PBS
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: EXPI 293F / Plasmid: pHLsec
Buffer solutionpH: 7.4 / Details: 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMsodium chlorideNaCl1
22.7 mMpotassium chlorideKCl1
34.3 mMDisodium phosphateNa2HPO1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: current: 30mA / Grid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Calibrated magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.43 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 601
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9PHENIXdev_5294model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 301423
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21000 / Symmetry type: POINT
Atomic model buildingB value: 60 / Protocol: OTHER / Space: REAL / Target criteria: FSC at 0.5
Atomic model buildingPDB-ID: 7A5V

7a5v


Accession code: 7A5V / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.96 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002114675
ELECTRON MICROSCOPYf_angle_d0.409519980
ELECTRON MICROSCOPYf_chiral_restr0.03982360
ELECTRON MICROSCOPYf_plane_restr0.0032455
ELECTRON MICROSCOPYf_dihedral_angle_d8.52525425
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.41840737371E-11
ens_1d_3CCELECTRON MICROSCOPYNCS constraints7.65436965347E-11
ens_1d_4CCELECTRON MICROSCOPYNCS constraints4.08236955928E-12
ens_1d_5CCELECTRON MICROSCOPYNCS constraints1.85551722166E-11
ens_2d_2NeELECTRON MICROSCOPYNCS constraints9.55039733001E-14
ens_2d_3NeELECTRON MICROSCOPYNCS constraints1.06638514424E-12
ens_2d_4NeELECTRON MICROSCOPYNCS constraints5.54857930813E-12
ens_2d_5NeELECTRON MICROSCOPYNCS constraints1.99663422443E-10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more