9FFT | pdb_00009fft

Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived asymmetric desensitised state of branch 2

• PDB DOI: https://doi.org/10.2210/pdb9FFT/pdb
• EM Map EMD-50373: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Lama glama, Helicobacter pylori G27
• 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived asymmetric desensitised state of branch 2

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A5B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 293.38 kDa 
• Atom Count: 14,939 
• Modeled Residue Count: 1,784 
• Deposited Residue Count: 2,529 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-1	A [auth D], D [auth A]	411	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P14867-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	B [auth E], C [auth B], E [auth C]	395	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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P28472-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody25,Outer membrane protein	F	522	Lama glama, Helicobacter pylori G27	Mutation(s): 0
UniProt
Find proteins for B5Z8H1 (Helicobacter pylori (strain G27)) Explore B5Z8H1  Go to UniProtKB:  B5Z8H1

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	G [auth a], H [auth b], J [auth c], L [auth d], M [auth e]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G], K [auth H], N [auth I]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ABU (Subject of Investigation/LOI)	O [auth D], P [auth B]	GAMMA-AMINO-BUTANOIC ACID C4 H9 N O2 BTCSSZJGUNDROE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Mihaylov, D.B., Malinauskas, T., Aricescu, A.R.

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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

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release