9HNT | pdb_00009hnt

a5b3 GABAAR bound to Etomidate, GABA, and Mb25 in a desensitized state in saposin nanodiscs

PDB DOI: https://doi.org/10.2210/pdb9HNT/pdb
EM Map EMD-52315: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Aequorea victoria, Homo sapiens, Escherichia coli
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2024-12-11 Released: 2025-12-24
Deposition Author(s): Cowgill, J., Fan, C., Howard, R.J., Lindahl, E.
Funding Organization(s): Swedish Research Council, European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9HNT

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

Literature

a5b3 GABAAR bound to Etomidate, GABA, and Mb25 in a desensitized state in saposin nanodiscs

Cowgill, J., Fan, C., Howard, R.J., Lindahl, E.

To be published.

Macromolecule Content

Total Structure Weight: 431.48 kDa
Atom Count: 15,197
Modeled Residue Count: 1,815
Deposited Residue Count: 3,768
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5	A, D	679	Aequorea victoria, Homo sapiens	Mutation(s): 0 Gene Names: GFP, GABRA5
UniProt & NIH Common Fund Data Resources
Find proteins for P31644 (Homo sapiens) Explore P31644 Go to UniProtKB: P31644
PHAROS: P31644 GTEx: ENSG00000186297
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31644
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain D	Go to GlyGen: P31644-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein	B, C, E	623	Homo sapiens, Aequorea victoria	Mutation(s): 0 Gene Names: GABRB3, GFP
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 C Focus chain E	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody 25	F [auth P]	541	Escherichia coli	Mutation(s): 0

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth F]	2		N-Glycosylation	Interactions Focus chain G [auth F] Interactions & Density Focus chain G [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth G], I [auth H], O [auth N]	3		N-Glycosylation	Interactions Focus chain H [auth G] Focus chain I [auth H] Focus chain O [auth N] Interactions & Density Focus chain H [auth G] Focus chain I [auth H] Focus chain O [auth N]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], N [auth M]	6		N-Glycosylation	Interactions Focus chain J [auth I] Focus chain N [auth M] Interactions & Density Focus chain J [auth I] Focus chain N [auth M]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J]	6		N-Glycosylation	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]

Entity ID: 8
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	L [auth K]	3		N-Glycosylation	Interactions Focus chain L [auth K] Interactions & Density Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G44266EX GlyCosmos: G44266EX GlyGen: G44266EX

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth L]	2		N-Glycosylation	Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]
Glycosylation Resources
GlyTouCan: G35932AR GlyCosmos: G35932AR GlyGen: G35932AR

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V8D (Subject of Investigation/LOI) Query on V8D Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain P [auth A] MOL2 format, chain T [auth E] MOL2 format, chain P [auth A] mmCIF format, chain T [auth E] mmCIF format, chain P [auth A]	P [auth A], T [auth E]	Etomidate C₁₄ H₁₆ N₂ O₂ NPUKDXXFDDZOKR-LLVKDONJSA-N		Interactions Focus chain P [auth A] Focus chain T [auth E] Interactions & Density Focus chain P [auth A] Focus chain T [auth E]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]
ABU (Subject of Investigation/LOI) Query on ABU Download:Ideal Coordinates CCD File SDF format, chain U [auth E] SDF format, chain Q [auth B] MOL2 format, chain U [auth E] MOL2 format, chain Q [auth B] mmCIF format, chain U [auth E] mmCIF format, chain Q [auth B]	Q [auth B], U [auth E]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain U [auth E] Interactions & Density Focus chain Q [auth B] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.32 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--
European Molecular Biology Organization (EMBO)	European Union	ALTF 542-2021

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.