9FAX | pdb_00009fax

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state

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

  • 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: 2.90 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 beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state

Kasaragod, V.B., Aricescu, A.R.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2A [auth E],
G [auth C]		405Homo sapiensMutation(s): 0 
Gene Names: GABRG2
Membrane Entity: Yes 
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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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neuroligin-2B [auth G],
H		33Homo sapiensMutation(s): 0 
Gene Names: NLGN2, KIAA1366
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFZ4 (Homo sapiens)
Explore Q8NFZ4 
Go to UniProtKB:  Q8NFZ4
PHAROS:  Q8NFZ4
GTEx:  ENSG00000169992 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NFZ4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
LHFPL tetraspan subfamily member 4 proteinC [auth I],
I [auth L]		188Homo sapiensMutation(s): 0 
Gene Names: LHFPL4, GARLH4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z7J7 (Homo sapiens)
Explore Q7Z7J7 
Go to UniProtKB:  Q7Z7J7
PHAROS:  Q7Z7J7
GTEx:  ENSG00000156959 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z7J7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3D [auth B],
E [auth A],
F [auth D]		439Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28472
Glycosylation
Glycosylation Sites: 1
Go to GlyGen: P28472-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Megabody25J [auth F]522Lama glamaMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseK [auth J]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 7
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-glucopyranoseL [auth K],
N		3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
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
M
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 10
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-glucopyranose
P
5N/A
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGW
Query on PGW
Download Ideal Coordinates CCD File 
AB [auth C],
BB [auth L],
W [auth I],
X [auth I]		(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
PX2
Query on PX2
Download Ideal Coordinates CCD File 
T [auth E],
Y [auth B]		1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
C27 H52 O8 P
OKLASJZQBDJAPH-RUZDIDTESA-M
CLR (Subject of Investigation/LOI)
Query on CLR
Download Ideal Coordinates CCD File 
U [auth E],
ZA [auth C]		CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM
Query on PLM
Download Ideal Coordinates CCD File 
EA [auth A],
LA [auth D],
QA [auth D],
WA [auth C],
XA [auth C]		PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
R16
Query on R16
Download Ideal Coordinates CCD File 
R [auth E],
S [auth E],
UA [auth C],
V [auth E],
VA [auth C]		HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
Q [auth E],
TA [auth C]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
D10
Query on D10
Download Ideal Coordinates CCD File 
BA [auth B],
DA [auth B],
KA [auth D],
MA [auth D],
NA [auth D]		DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
HEX
Query on HEX
Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth B]
FA [auth A]
GA [auth A]
HA [auth A]
AA [auth B],
CA [auth B],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
OA [auth D],
PA [auth D],
RA [auth D],
SA [auth D],
YA [auth C],
Z [auth B]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
P1L
Query on P1L		A [auth E],
G [auth C]		L-PEPTIDE LINKINGC19 H37 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.40
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