9FAT | pdb_00009fat

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, Megabody38 and pregnenolone sulfate

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens, Lama glama
  • Expression System: Homo sapiens, Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-05-10 Released: 2025-07-02 
  • 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: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, Megabody38 and pregnenolone sulfate

Kasaragod, V.B., Aricescu, A.R.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-1
A, D
413Homo sapiensMutation(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  
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UniProt GroupP14867
Glycosylation
Glycosylation Sites: 1
Go to GlyGen: P14867-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3
B, E
441Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28472
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: P28472-1
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2405Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18507
Glycosylation
Glycosylation Sites: 1
Go to GlyGen: P18507-2
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Megabody38F [auth G]539Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Neuroligin-2G [auth H]33Homo sapiensMutation(s): 0 
Gene Names: NLGN2, KIAA1366
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFZ4 (Homo sapiens)
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Go to UniProtKB:  Q8NFZ4
PHAROS:  Q8NFZ4
GTEx:  ENSG00000169992 
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UniProt GroupQ8NFZ4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
LHFPL tetraspan subfamily member 4 proteinH [auth L]190Homo sapiensMutation(s): 0 
Gene Names: LHFPL4, GARLH4
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7J7 (Homo sapiens)
Explore Q7Z7J7 
Go to UniProtKB:  Q7Z7J7
PHAROS:  Q7Z7J7
GTEx:  ENSG00000156959 
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UniProt GroupQ7Z7J7
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Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseI [auth F]10N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU
GlyCosmos:  G40702WU
GlyGen:  G40702WU
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseJ [auth I]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J],
O		3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth K]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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
M
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G23799GS
GlyCosmos:  G23799GS
GlyGen:  G23799GS
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D 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
N
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGW
Query on PGW
Download Ideal Coordinates CCD File 
FA [auth L],
Q [auth A],
W [auth B]		(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
PIO
Query on PIO
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CA [auth D],
P [auth A]		[(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
PX2
Query on PX2
Download Ideal Coordinates CCD File 
AA [auth D]1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
C27 H52 O8 P
OKLASJZQBDJAPH-RUZDIDTESA-M
A8W (Subject of Investigation/LOI)
Query on A8W
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BA [auth D]Pregnenolone sulfate
C21 H32 O5 S
DIJBBUIOWGGQOP-QGVNFLHTSA-N
CLR (Subject of Investigation/LOI)
Query on CLR
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Y [auth C]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM
Query on PLM
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X [auth C]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
R16
Query on R16
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T [auth B]HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
D10
Query on D10
Download Ideal Coordinates CCD File 
R [auth A],
U [auth B],
Z [auth C]		DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
HEX
Query on HEX
Download Ideal Coordinates CCD File 
DA [auth D],
EA [auth E],
V [auth B]		HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
GA [auth L],
S [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
P1L
Query on P1L
C
L-PEPTIDE LINKINGC19 H37 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX19.2

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/15
European Molecular Biology Organization (EMBO)European UnionALTF137-2019
H2020 Marie Curie Actions of the European CommissionEuropean UnionGABAARComp-897707
Medical Research Council (MRC, United Kingdom)United KingdomMR/L009609/1
Medical Research Council (MRC, United Kingdom)United KingdomMC_EX_MR/T046279/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01-GM135550
National Science Foundation (NSF, United States)United StatesNeuroNex 2014862

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release