9FFL | pdb_00009ffl

Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived symmetric bound-closed state

PDB DOI: https://doi.org/10.2210/pdb9FFL/pdb
EM Map EMD-50365: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Lama glama, Helicobacter pylori G27
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: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in the short-lived symmetric pre-active state

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

To be published.

Macromolecule Content

Total Structure Weight: 296.05 kDa
Atom Count: 15,223
Modeled Residue Count: 1,784
Deposited Residue Count: 2,529
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

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 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14867
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth D] Focus chain D [auth A]	Go to GlyGen: P14867-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28472
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth E] Focus chain C [auth B] Focus chain E [auth C]	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody25,Outer membrane protein	F	522	Lama glama, Helicobacter pylori G27	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B5Z8H1 (Helicobacter pylori (strain G27)) Explore B5Z8H1 Go to UniProtKB: B5Z8H1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5Z8H1
Sequence Annotations Expand
Reference Sequence

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	Interactions Focus chain G [auth a] Focus chain H [auth b] Focus chain J [auth c] Focus chain L [auth d] Focus chain M [auth e] Interactions & Density Focus chain G [auth a] Focus chain H [auth b] Focus chain J [auth c] Focus chain L [auth d] Focus chain M [auth e]
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	Interactions Focus chain I [auth G] Focus chain K [auth H] Focus chain N [auth I] Interactions & Density Focus chain I [auth G] Focus chain K [auth H] Focus chain N [auth I]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain P [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain P [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain P [auth D]	P [auth D], Y [auth A]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain P [auth D] Focus chain Y [auth A] Interactions & Density Focus chain P [auth D] Focus chain Y [auth A]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain S [auth E] SDF format, chain O [auth D] SDF format, chain AA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [auth E] MOL2 format, chain O [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [auth E] mmCIF format, chain O [auth D] mmCIF format, chain AA [auth C]	AA [auth C] O [auth D] S [auth E] U [auth B] V [auth B] AA [auth C], O [auth D], S [auth E], U [auth B], V [auth B], X [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain O [auth D] Focus chain S [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth B] Interactions & Density Focus chain AA [auth C] Focus chain O [auth D] Focus chain S [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth B]
ABU (Subject of Investigation/LOI) Query on ABU Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain R [auth E] MOL2 format, chain T [auth B] MOL2 format, chain R [auth E] mmCIF format, chain T [auth B] mmCIF format, chain R [auth E]	R [auth E], T [auth B]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain R [auth E] Focus chain T [auth B] Interactions & Density Focus chain R [auth E] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Q [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain Q [auth D] mmCIF format, chain Z [auth A] mmCIF format, chain Q [auth D]	Q [auth D], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth D] Focus chain Z [auth A] Interactions & Density Focus chain Q [auth D] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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

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