9SLM | pdb_00009slm

GABA-A a4b3d receptor in complex with GABA and Nb24

PDB DOI: https://doi.org/10.2210/pdb9SLM/pdb
EM Map EMD-55007: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Lama glama
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-09-04 Released: 2026-09-02
Deposition Author(s): Nestorow, S., Miller, P.S.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), F. Hoffmann-La Roche LTD

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Molecular arrangement and modulation of extrasynaptic alpha beta delta GABAA receptors

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.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-76879-5

Macromolecule Content

Total Structure Weight: 266.06 kDa
Atom Count: 15,621
Modeled Residue Count: 1,907
Deposited Residue Count: 2,306
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-4,Gamma-aminobutyric acid type A receptor subunit alpha4	A, C	364	Homo sapiens	Mutation(s): 1 Gene Names: Gabra4, GABRA4
UniProt
Find proteins for Q9D6F4 (Mus musculus) Explore Q9D6F4 Go to UniProtKB: Q9D6F4
Find proteins for F6UBA8 (Equus caballus) Explore F6UBA8 Go to UniProtKB: F6UBA8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q9D6F4 F6UBA8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C	Go to GlyGen: Q9D6F4-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	B, D	451	Homo sapiens	Mutation(s): 0 Gene Names: GABRB3
UniProt & NIH Common Fund Data Resources
Find proteins for P28472 (Homo sapiens) Explore P28472 Go to UniProtKB: P28472
PHAROS: P28472 GTEx: ENSG00000166206
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28472
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain D	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit delta	E	430	Homo sapiens	Mutation(s): 0 Gene Names: GABRD
UniProt & NIH Common Fund Data Resources
Find proteins for O14764 (Homo sapiens) Explore O14764 Go to UniProtKB: O14764
PHAROS: O14764 GTEx: ENSG00000187730
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14764
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E	Go to GlyGen: O14764-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Nb24	F, G	123	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth O]	2		N/A	Interactions Focus chain H [auth O] Interactions & Density Focus chain H [auth O]

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth P]	3		N-Glycosylation	Interactions Focus chain I [auth P] Interactions & Density Focus chain I [auth P]

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX6 Query on PX6 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE C₃₅ H₆₈ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-M		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain T [auth C] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain T [auth C] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain T [auth C] mmCIF format, chain K [auth A]	J [auth A] K [auth A] P [auth B] Q [auth B] R [auth B] J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B], T [auth C], V [auth D], X [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain X [auth E]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth D] SDF format, chain S [auth B] SDF format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain W [auth D] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain W [auth D] mmCIF format, chain S [auth B] mmCIF format, chain L [auth A]	L [auth A], N [auth A], S [auth B], W [auth D]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain W [auth D] Interactions & Density Focus chain L [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain W [auth D]
ABU (Subject of Investigation/LOI) Query on ABU Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth B] MOL2 format, chain U [auth D] MOL2 format, chain O [auth B] mmCIF format, chain U [auth D] mmCIF format, chain O [auth B]	O [auth B], U [auth D]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain U [auth D] Interactions & Density Focus chain O [auth B] Focus chain U [auth D]