9FGF | pdb_00009fgf

Cryo-EM structure of the full-length alpha1beta3gamma2 GABA(A) receptor in Saposin A nanodisc in the long-lived symmetric resting state

PDB DOI: https://doi.org/10.2210/pdb9FGF/pdb
EM Map EMD-50399: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
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: 2.90 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 in the long-lived symmetric resting state

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

To be published.

Macromolecule Content

Total Structure Weight: 280.09 kDa
Atom Count: 14,359
Modeled Residue Count: 1,686
Deposited Residue Count: 2,369
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, 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18507
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C	Go to GlyGen: P18507-2
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	F [auth d]	5		N-Glycosylation	Interactions Focus chain F [auth d] Interactions & Density Focus chain F [auth d]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 a]	9		N-Glycosylation	Interactions Focus chain G [auth a] Interactions & Density Focus chain G [auth a]
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth b], J [auth e]	2		N-Glycosylation	Interactions Focus chain H [auth b] Focus chain J [auth e] Interactions & Density Focus chain H [auth b] Focus chain J [auth e]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 F], K [auth G]	6		N-Glycosylation	Interactions Focus chain I [auth F] Focus chain K [auth G] Interactions & Density Focus chain I [auth F] Focus chain K [auth G]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIO Query on PIO Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain U [auth D] MOL2 format, chain M [auth A] MOL2 format, chain U [auth D] mmCIF format, chain M [auth A] mmCIF format, chain U [auth D]	M [auth A], U [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 U [auth D] Interactions & Density Focus chain M [auth A] Focus chain U [auth D]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain V [auth D] MOL2 format, chain N [auth A] MOL2 format, chain V [auth D] mmCIF format, chain N [auth A] mmCIF format, chain V [auth D]	N [auth A], V [auth D]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain V [auth D] Interactions & Density Focus chain N [auth A] Focus chain V [auth D]
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth E] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth E] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth E]	O [auth A], P [auth B], S [auth C], W [auth D], X [auth E]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth E] Interactions & Density Focus chain O [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	L [auth A], Q [auth C], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain L [auth A] Focus chain Q [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	RELION

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