9FGG | pdb_00009fgg

Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in Saposin A nanodisc bound to GABA and Etomidate in the long-lived symmetric desensitised state

PDB DOI: https://doi.org/10.2210/pdb9FGG/pdb
EM Map EMD-50400: EMDB EMDataResource

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

Deposited: 2024-05-23 Released: 2025-06-04
Deposition Author(s): Mihaylov, D.B., Malinauskas, T., Aricescu, A.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Cancer Research UK, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 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

Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in Saposin A nanodisc bound to GABA and Etomidate in the long-lived symmetric desensitised state

Mihaylov, D.B., Malinauskas, T., Aricescu, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 295.48 kDa
Atom Count: 15,200
Modeled Residue Count: 1,793
Deposited Residue Count: 2,502
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-1	A, D	464	Homo sapiens	Mutation(s): 0 Gene Names: GABRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P14867 (Homo sapiens) Explore P14867 Go to UniProtKB: P14867
PHAROS: P14867 GTEx: ENSG00000022355
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14867
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain D	Go to GlyGen: P14867-1
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, E	473	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 E	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 gamma-2	C	495	Homo sapiens	Mutation(s): 0 Gene Names: GABRG2
UniProt & NIH Common Fund Data Resources
Find proteins for P18507 (Homo sapiens) Explore P18507 Go to UniProtKB: P18507
PHAROS: P18507 GTEx: ENSG00000113327
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18507
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C	Go to GlyGen: P18507-2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody-38	F [auth G]	133	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	G [auth F]	9		N-Glycosylation	Interactions Focus chain G [auth F] Interactions & Density Focus chain G [auth F]
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, K	2		N-Glycosylation	Interactions Focus chain H Focus chain K Interactions & Density Focus chain H Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, L	6		N-Glycosylation	Interactions Focus chain I Focus chain L Interactions & Density Focus chain I Focus chain L
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	J	5		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIO Query on PIO Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain M [auth A] MOL2 format, chain V [auth D] MOL2 format, chain M [auth A] mmCIF format, chain V [auth D] mmCIF format, chain M [auth A]	M [auth A], V [auth D]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain M [auth A] Focus chain V [auth D] Interactions & Density Focus chain M [auth A] Focus chain V [auth D]
V8D (Subject of Investigation/LOI) Query on V8D Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain BA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain BA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain BA [auth E]	BA [auth E], Q [auth B]	Etomidate C₁₄ H₁₆ N₂ O₂ NPUKDXXFDDZOKR-LLVKDONJSA-N		Interactions Focus chain BA [auth E] Focus chain Q [auth B] Interactions & Density Focus chain BA [auth E] Focus chain Q [auth B]
R16 Query on R16 Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain AA [auth E]	AA [auth E]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Interactions & Density Focus chain AA [auth E]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain N [auth A] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A]	N [auth A], R [auth B], T [auth C], W [auth D], Z [auth E]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain N [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E]
ABU (Subject of Investigation/LOI) Query on ABU Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain P [auth B] MOL2 format, chain Y [auth E] MOL2 format, chain P [auth B] mmCIF format, chain Y [auth E] mmCIF format, chain P [auth B]	P [auth B], Y [auth E]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain Y [auth E] Interactions & Density Focus chain P [auth B] Focus chain Y [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain O [auth A] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain O [auth A] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain O [auth A]	O [auth A], U [auth C], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth A] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain O [auth A] Focus chain U [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	RELION

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Mihaylov, D.B.

Malinauskas, T.

Aricescu, A.R.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/15
Cancer Research UK	United Kingdom	DRCRPG-May23/100002
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L009609/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_EX_MR/T046279/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01-GM135550
National Science Foundation (NSF, United States)	United States	NeuroNex 2014862