9FFZ | pdb_00009ffz

Cryo-EM structure of the alpha1beta3gamma2 GABA(A) receptor in complex with GABA and Nb38 in the short-lived asymmetric desensitised 1 state

PDB DOI: https://doi.org/10.2210/pdb9FFZ/pdb
EM Map EMD-50379: EMDB EMDataResource

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

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: 3.30 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 alpha1beta3gamma2 GABA(A) receptor in complex with GABA and Nb38 in the short-lived asymmetric desensitised 1 state

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

To be published.

Macromolecule Content

Total Structure Weight: 250.5 kDa
Atom Count: 15,101
Modeled Residue Count: 1,799
Deposited Residue Count: 2,118
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	411	Homo sapiens	Mutation(s): 0 Gene Names: GABRA1 Membrane Entity: Yes
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	395	Homo sapiens	Mutation(s): 0 Gene Names: GABRB3 Membrane Entity: Yes
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
Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2	C	373	Homo sapiens	Mutation(s): 0 Gene Names: GABRG2 Membrane Entity: Yes
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
Nanobody38	F	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-(1-2)-alpha-D-mannopyranose-(1-6)-[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	G [auth a]	10		N-Glycosylation	Interactions Focus chain G [auth a] Interactions & Density Focus chain G [auth a]
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

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 [auth b], J [auth c], L [auth e]	2		N-Glycosylation	Interactions Focus chain H [auth b] Focus chain J [auth c] Focus chain L [auth e] Interactions & Density Focus chain H [auth b] Focus chain J [auth c] Focus chain L [auth e]
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 [auth G], M [auth H]	6		N-Glycosylation	Interactions Focus chain I [auth G] Focus chain M [auth H] Interactions & Density Focus chain I [auth G] Focus chain M [auth H]
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	K [auth d]	5		N-Glycosylation	Interactions Focus chain K [auth d] Interactions & Density Focus chain K [auth d]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D3D Query on D3D Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	(19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-UCZVXENKSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
ABU (Subject of Investigation/LOI) Query on ABU Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain N [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth A]	N [auth A], Q [auth E]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Q [auth E] Interactions & Density Focus chain N [auth A] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

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