9FAS | pdb_00009fas

CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate

PDB DOI: https://doi.org/10.2210/pdb9FAS/pdb
EM Map EMD-50280: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-05-10 Released: 2025-05-28
Deposition Author(s): Kasaragod, V.B., Aricescu, A.R.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Molecular Biology Organization (EMBO), H2020 Marie Curie Actions of the European Commission, 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: 2.50 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

CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate

Kasaragod, V.B., Aricescu, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 259.23 kDa
Atom Count: 15,501
Modeled Residue Count: 1,726
Deposited Residue Count: 2,112
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit alpha-1	A, D	409	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	B, E	441	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: 1	Glycosylation Focus chain B Focus chain E	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
Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2	C	412	Homo sapiens	Mutation(s): 0 Gene Names: GABRG2
UniProt & NIH Common Fund Data Resources
Find proteins for P18507 (Homo sapiens) Go to UniProtKB: P18507
PHAROS: P18507 GTEx: ENSG00000113327
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18507-2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
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-(1-2)-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	F	10		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, K	3		N-Glycosylation	Interactions Focus chain G Focus chain K Interactions & Density Focus chain G Focus chain K

Entity ID: 6
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	H, J	6		N-Glycosylation	Interactions Focus chain H Focus chain J Interactions & Density Focus chain H Focus chain J

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	I	6		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW Query on PGW Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain OA [auth D] SDF format, chain R [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain R [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain R [auth A]	N [auth A], OA [auth D], R [auth A]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain N [auth A] Focus chain OA [auth D] Focus chain R [auth A] Interactions & Density Focus chain N [auth A] Focus chain OA [auth D] Focus chain R [auth A]
PIO Query on PIO Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D]	M [auth A], MA [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 MA [auth D] Interactions & Density Focus chain M [auth A] Focus chain MA [auth D]
PX2 Query on PX2 Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE C₂₇ H₅₂ O₈ P OKLASJZQBDJAPH-RUZDIDTESA-M		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
A8W (Subject of Investigation/LOI) Query on A8W Download Ideal Coordinates CCD File SDF format, chain GA [auth C] MOL2 format, chain GA [auth C] mmCIF format, chain GA [auth C]	GA [auth C]	Pregnenolone sulfate C₂₁ H₃₂ O₅ S DIJBBUIOWGGQOP-QGVNFLHTSA-N		Interactions Focus chain GA [auth C] Interactions & Density Focus chain GA [auth C]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain KA [auth C] SDF format, chain S [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain S [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain S [auth A]	EA [auth C], KA [auth C], S [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain KA [auth C] Focus chain S [auth A] Interactions & Density Focus chain EA [auth C] Focus chain KA [auth C] Focus chain S [auth A]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain TA [auth D] SDF format, chain W [auth B] SDF format, chain XA [auth E] SDF format, chain Z [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain TA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain Z [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain TA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain Z [auth B]	AB [auth E], TA [auth D], W [auth B], XA [auth E], Z [auth B]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain TA [auth D] Focus chain W [auth B] Focus chain XA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain AB [auth E] Focus chain TA [auth D] Focus chain W [auth B] Focus chain XA [auth E] Focus chain Z [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain HA [auth C] MOL2 format, chain HA [auth C] mmCIF format, chain HA [auth C]	HA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain HA [auth C] Interactions & Density Focus chain HA [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain BB [auth E] SDF format, chain FA [auth C] SDF format, chain JA [auth C] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain T [auth A] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain X [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain P [auth A] SDF format, chain YA [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain YA [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain YA [auth E]	BA [auth B] BB [auth E] CA [auth B] DA [auth B] FA [auth C] BA [auth B], BB [auth E], CA [auth B], DA [auth B], FA [auth C], JA [auth C], O [auth A], P [auth A], Q [auth A], QA [auth D], RA [auth D], SA [auth D], T [auth A], UA [auth D], VA [auth D], X [auth B], YA [auth E]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain BB [auth E] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain JA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain X [auth B] Focus chain YA [auth E] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth E] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth C] Focus chain JA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain X [auth B] Focus chain YA [auth E]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CB [auth E] SDF format, chain IA [auth C] SDF format, chain L [auth A] SDF format, chain NA [auth D] SDF format, chain PA [auth D] SDF format, chain Y [auth B] SDF format, chain ZA [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain CB [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth E] mmCIF format, chain AA [auth B] mmCIF format, chain CB [auth E] mmCIF format, chain IA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain ZA [auth E]	AA [auth B] CB [auth E] IA [auth C] L [auth A] NA [auth D] AA [auth B], CB [auth E], IA [auth C], L [auth A], NA [auth D], PA [auth D], Y [auth B], ZA [auth E]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CB [auth E] Focus chain IA [auth C] Focus chain L [auth A] Focus chain NA [auth D] Focus chain PA [auth D] Focus chain Y [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain CB [auth E] Focus chain IA [auth C] Focus chain L [auth A] Focus chain NA [auth D] Focus chain PA [auth D] Focus chain Y [auth B] Focus chain ZA [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain U [auth A] SDF format, chain WA [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain WA [auth D] mmCIF format, chain LA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain WA [auth D]	LA [auth C], U [auth A], WA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain LA [auth C] Focus chain U [auth A] Focus chain WA [auth D] Interactions & Density Focus chain LA [auth C] Focus chain U [auth A] Focus chain WA [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.40
MODEL REFINEMENT	PHENIX	19.2

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

Kasaragod, V.B.

Aricescu, A.R.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/15
European Molecular Biology Organization (EMBO)	European Union	ALTF137-2019
H2020 Marie Curie Actions of the European Commission	European Union	GABAARComp-897707
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