[English] 日本語
Yorodumi
- PDB-9sld: GABA-A a4b3d receptor in complex with DS2-Me, GABA, Nb24 and Mb30 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9sld
TitleGABA-A a4b3d receptor in complex with DS2-Me, GABA, Nb24 and Mb30
Components
  • (Gamma-aminobutyric acid receptor subunit ...) x 3
  • Megabody Mb30
  • Nanobody Nb24
KeywordsMEMBRANE PROTEIN / pLGIC / GABA / Neurotransmission / Extrasynaptic
Function / homology
Function and homology information


benzodiazepine receptor activity / extrasynaptic signaling via GABA / cellular response to histamine / inner ear receptor cell development / GABA receptor activation / negative regulation of synaptic transmission, GABAergic / innervation / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly ...benzodiazepine receptor activity / extrasynaptic signaling via GABA / cellular response to histamine / inner ear receptor cell development / GABA receptor activation / negative regulation of synaptic transmission, GABAergic / innervation / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / GABA-A receptor activity / roof of mouth development / inhibitory postsynaptic potential / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / chloride channel activity / Signaling by ERBB4 / cochlea development / chloride channel complex / cytoplasmic vesicle membrane / dendrite membrane / chloride transmembrane transport / electron transport chain / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / dendritic spine / electron transfer activity / periplasmic space / postsynaptic membrane / postsynapse / iron ion binding / axon / neuronal cell body / heme binding / dendrite / glutamatergic synapse / cell surface / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 4 subunit / Gamma-aminobutyric-acid A receptor delta 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 ...Gamma-aminobutyric-acid A receptor, alpha 4 subunit / Gamma-aminobutyric-acid A receptor delta 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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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-AMINO-BUTANOIC ACID / DECANE / Gamma-aminobutyric acid receptor subunit delta / Soluble cytochrome b562 / Gamma-aminobutyric acid receptor subunit beta-3 / Gamma-aminobutyric acid receptor subunit alpha-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsNestorow, S. / Miller, P.S.
Funding support United Kingdom, Switzerland, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M024709/1 United Kingdom
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Molecular arrangement and modulation of extrasynaptic alpha beta delta GABAA receptors
Authors: Nestorow, S.A. / Chen, W.N. / Bertrand, D. / Wahid, A.A. / Wyatt, C.E. / Mortensen, M. / Clairfeuille, T. / Reutlinger, M. / Friz, G. / Pardon, E. / Steyaert, J. / Ladds, G. / Cecere, G. / ...Authors: Nestorow, S.A. / Chen, W.N. / Bertrand, D. / Wahid, A.A. / Wyatt, C.E. / Mortensen, M. / Clairfeuille, T. / Reutlinger, M. / Friz, G. / Pardon, E. / Steyaert, J. / Ladds, G. / Cecere, G. / Smart, T.G. / Hernandez, M.C. / Joedicke, L. / Miller, P.S.
History
DepositionSep 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor subunit alpha-4
B: Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrome b562
C: Gamma-aminobutyric acid receptor subunit alpha-4
D: Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrome b562
E: Gamma-aminobutyric acid receptor subunit delta
F: Megabody Mb30
G: Nanobody Nb24
H: Megabody Mb30
I: Nanobody Nb24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,82624
Polymers295,1839
Non-polymers3,64415
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Gamma-aminobutyric acid receptor subunit ... , 3 types, 5 molecules ACBDE

#1: Protein Gamma-aminobutyric acid receptor subunit alpha-4 / GABA(A) receptor subunit alpha-4 / GABAAR subunit alpha-4


Mass: 41783.336 Da / Num. of mol.: 2 / Mutation: M120T
Source method: isolated from a genetically manipulated source
Details: Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRA4 / Production host: Homo sapiens (human) / References: UniProt: P48169
#2: Protein Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrome b562 / GABA(A) receptor subunit beta-3 / GABAAR subunit beta-3 / Cytochrome b-562


Mass: 51615.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Modified glvi sequence containing the Escherichia coli soluble cytochrome B562RIL41 (BRIL, amino acids 23-130, ADLE...QKYL, Uniprot P0ABE7) to give the sequence SQPAGT-BRIL-TGRAA. Linker ...Details: Modified glvi sequence containing the Escherichia coli soluble cytochrome B562RIL41 (BRIL, amino acids 23-130, ADLE...QKYL, Uniprot P0ABE7) to give the sequence SQPAGT-BRIL-TGRAA. Linker regions substituted Gly308-Asn421. This BRIL domain was present in the protein but not resolved in the cryo-EM density and is therefore not included in the atomic model,Modified glvi sequence containing the Escherichia coli soluble cytochrome B562RIL41 (BRIL, amino acids 23-130, ADLE...QKYL, Uniprot P0ABE7) to give the sequence SQPAGT-BRIL-TGRAA. Linker regions substituted Gly308-Asn421. This BRIL domain was present in the protein but not resolved in the cryo-EM density and is therefore not included in the atomic model,Modified glvi sequence containing the Escherichia coli soluble cytochrome B562RIL41 (BRIL, amino acids 23-130, ADLE...QKYL, Uniprot P0ABE7) to give the sequence SQPAGT-BRIL-TGRAA. Linker regions substituted Gly308-Asn421. This BRIL domain was present in the protein but not resolved in the cryo-EM density and is therefore not included in the atomic model,Modified glvi sequence containing the Escherichia coli soluble cytochrome B562RIL41 (BRIL, amino acids 23-130, ADLE...QKYL, Uniprot P0ABE7) to give the sequence SQPAGT-BRIL-TGRAA. Linker regions substituted Gly308-Asn421. This BRIL domain was present in the protein but not resolved in the cryo-EM density and is therefore not included in the atomic model
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: GABRB3, cybC / Production host: Homo sapiens (human) / References: UniProt: P28472, UniProt: P0ABE7
#3: Protein Gamma-aminobutyric acid receptor subunit delta / GABA(A) receptor subunit delta / GABAAR subunit delta


Mass: 48233.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start ...Details: Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRD / Production host: Homo sapiens (human) / References: UniProt: O14764

-
Antibody , 2 types, 4 molecules FHGI

#4: Antibody Megabody Mb30


Mass: 15386.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This nanobody was expressed as part of a megabody fusion construct. The scaffold domain of the megabody was present in the construct but was disordered in the cryo-EM density and therefore ...Details: This nanobody was expressed as part of a megabody fusion construct. The scaffold domain of the megabody was present in the construct but was disordered in the cryo-EM density and therefore not included in the atomic model. Only the nanobody sequence is provided in the deposited coordinates.
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#5: Antibody Nanobody Nb24


Mass: 14689.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)

-
Sugars , 3 types, 8 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#8: 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.: 6 / 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 , 3 types, 7 molecules

#9: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, inhibitor*YM
#10: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22
#11: Chemical ChemComp-A1JOJ / 4-chloranyl-~{N}-(6-methyl-2-thiophen-2-yl-imidazo[1,2-a]pyridin-3-yl)benzamide


Mass: 367.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H14ClN3OS / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1alpha4-beta3-delta GABA-A receptor in complex with DS2-Me, GABA, nanobody Nb24 and megabody Mb30COMPLEXThe heteropentameric alpha4beta3delta GABA(A) receptor was recombinantly expressed in Expi293 cells. Constructs were engineered with the M3- M4 intracellular domain replaced either by a GLVI linker sequence (SQPARAA) or by a modified GLVI sequence containing Escherichia coli cytochrome B562RIL41. The sample was prepared in the presence of DS2-Me, GABA, nanobody Nb24, and megabody Mb30.#1-#50MULTIPLE SOURCES
2GABA-A receptorCOMPLEX#1-#31RECOMBINANT
3Megabody Mb30COMPLEX#41RECOMBINANT
4Nanobody Nb24COMPLEX#51RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
41NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Lama glama (llama)9844
54Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Homo sapiens (human)9606
32Homo sapiens (human)9606Expi293F GnTI-pHLsec
43Escherichia coli (E. coli)562pBAD
54Homo sapiens (human)9606Expi293FpHLsec
Buffer solutionpH: 7.6
Details: 75 millimolar sodium chloride; 12.5 millimolar HEPES, pH 7.6; 10 millimolar biotin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Nanodisc-reconstituted alpha4beta3delta GABA-A receptor in complex with DS2-Me, GABA, nanobody Nb24 and megabody Mb30
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.39 sec. / Electron dose: 53.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 7912

-
Processing

EM software
IDNameVersionCategory
1ARP/wARP1.0.9particle selection
4ARP/wARP1.0.9CTF correction
7UCSF ChimeraX1.8model fitting
9PHENIX1.20.1_4487model refinement
10cryoSPARC4.4.1 to 4.7.1initial Euler assignment
11cryoSPARC4.4.1 to 4.7.1final Euler assignment
12cryoSPARC4.4.1 to 4.7.1classification
13cryoSPARC4.4.1 to 4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 689954
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110542 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7QN7

7qn7


Accession code: 7QN7 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217954
ELECTRON MICROSCOPYf_angle_d0.42624374
ELECTRON MICROSCOPYf_dihedral_angle_d4.3882537
ELECTRON MICROSCOPYf_chiral_restr0.042722
ELECTRON MICROSCOPYf_plane_restr0.0023038

+
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