9FAV | pdb_00009fav

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2 and Megabody25, in a closed state (StateC2)

  • 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: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9FAV

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 GARLH4, the TMD of Neuroligin2 and Megabody25, in a closed state (StateC2)

Kasaragod, V.B., Aricescu, A.R.

To be published.

Macromolecule Content 

  • Total Structure Weight: 453.82 kDa 
  • Atom Count: 18,975 
  • Modeled Residue Count: 2,240 
  • Deposited Residue Count: 3,945 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3A [auth B],
B [auth E],
C [auth A],
D		439Homo 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: 1
Go to GlyGen: P28472-1
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2E [auth C]405Homo 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
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuroligin-2F [auth H]33Homo sapiensMutation(s): 0 
Gene Names: NLGN2, KIAA1366
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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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
LHFPL tetraspan subfamily member 4 proteinG [auth L]185Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z7J7
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Megabody25H [auth K],
I [auth O],
J [auth F]		522Lama glamaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth G],
O [auth N]		3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseL [auth I]7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth J],
Q		2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseN [auth M]6N/A
Glycosylation Resources
GlyTouCan: G09724ZC
GlyCosmos: G09724ZC
GlyGen: G09724ZC
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranose
P
8N-Glycosylation
Glycosylation Resources
GlyTouCan: G34499SX
GlyCosmos: G34499SX
GlyGen: G34499SX
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD 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
R
5N/A
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGW

Query on PGW


Download:Ideal Coordinates CCD File
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
PX2

Query on PX2


Download:Ideal Coordinates CCD File
CA [auth D]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
HA [auth C]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
R16

Query on R16


Download:Ideal Coordinates CCD File
EA [auth C],
FA [auth C],
V [auth B]		HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
NAG

Query on NAG


Download:Ideal Coordinates CCD File
DA [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
AA [auth A],
GA [auth C],
U [auth B],
Z [auth E]		DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
HEX

Query on HEX


Download:Ideal Coordinates CCD File
BA [auth A],
S [auth B],
T [auth B],
X [auth E],
Y [auth E]		HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
P1L
Query on P1L		E [auth C]L-PEPTIDE LINKINGC19 H37 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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