9FAU | pdb_00009fau

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2 and Megabody25, in a closed state (StateC1)

PDB DOI: https://doi.org/10.2210/pdb9FAU/pdb
EM Map EMD-50282: EMDB EMDataResource

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: 3.10 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 beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2 and Megabody25, in a closed state (StateC1)

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

To be published.

Macromolecule Content

Total Structure Weight: 455.8 kDa
Atom Count: 19,115
Modeled Residue Count: 2,241
Deposited Residue Count: 3,947
Unique protein chains: 5

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 beta-3	A [auth B], B [auth E], C [auth A], D	439	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28472
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth B] Focus chain B [auth E] Focus chain C [auth A] Focus chain D	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2	E [auth C]	404	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18507
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E [auth C]	Go to GlyGen: P18507-2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroligin-2	F [auth H]	33	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NFZ4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
LHFPL tetraspan subfamily member 4 protein	G [auth L]	188	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z7J7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody25	H [auth K], I [auth O], J [auth F]	522	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	K [auth G]	7		N-Glycosylation	Interactions Focus chain K [auth G] Interactions & Density Focus chain K [auth G]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 7
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	L [auth I], P	3		N-Glycosylation	Interactions Focus chain L [auth I] Focus chain P Interactions & Density Focus chain L [auth I] Focus chain P
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth J], Q	2		N-Glycosylation	Interactions Focus chain M [auth J] Focus chain Q Interactions & Density Focus chain M [auth J] Focus chain Q
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
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	N [auth M], O [auth N]	6		N-Glycosylation	Interactions Focus chain N [auth M] Focus chain O [auth N] Interactions & Density Focus chain N [auth M] Focus chain O [auth N]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 10
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	R	5		N-Glycosylation	Interactions Focus chain R Interactions & Density Focus chain R
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW Query on PGW Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain NA [auth L] MOL2 format, chain V [auth B] MOL2 format, chain NA [auth L] mmCIF format, chain V [auth B] mmCIF format, chain NA [auth L]	NA [auth L], V [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		Interactions Focus chain NA [auth L] Focus chain V [auth B] Interactions & Density Focus chain NA [auth L] Focus chain V [auth B]
PX2 Query on PX2 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain EA [auth C]	EA [auth C]	1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE C₂₇ H₅₂ O₈ P OKLASJZQBDJAPH-RUZDIDTESA-M		Interactions Focus chain EA [auth C] Interactions & Density Focus chain EA [auth C]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain OA [auth L] MOL2 format, chain LA [auth C] MOL2 format, chain OA [auth L] mmCIF format, chain LA [auth C] mmCIF format, chain OA [auth L]	LA [auth C], OA [auth L]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain LA [auth C] Focus chain OA [auth L] Interactions & Density Focus chain LA [auth C] Focus chain OA [auth L]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain KA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain KA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain KA [auth C]	IA [auth C], KA [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain KA [auth C] Interactions & Density Focus chain IA [auth C] Focus chain KA [auth C]
R16 Query on R16 Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain JA [auth C]	GA [auth C], HA [auth C], JA [auth C]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth C] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain FA [auth C] MOL2 format, chain FA [auth C] mmCIF format, chain FA [auth C]	FA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FA [auth C] Interactions & Density Focus chain FA [auth C]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain MA [auth L] SDF format, chain U [auth B] SDF format, chain Y [auth E] SDF format, chain Z [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain MA [auth L] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain MA [auth L] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth A]	CA [auth D] DA [auth D] MA [auth L] U [auth B] Y [auth E] CA [auth D], DA [auth D], MA [auth L], U [auth B], Y [auth E], Z [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain MA [auth L] Focus chain U [auth B] Focus chain Y [auth E] Focus chain Z [auth A] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain MA [auth L] Focus chain U [auth B] Focus chain Y [auth E] Focus chain Z [auth A]
HEX Query on HEX Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain BA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain BA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain BA [auth A]	AA [auth A] BA [auth A] S [auth B] T [auth B] W [auth E] AA [auth A], BA [auth A], S [auth B], T [auth B], W [auth E], X [auth E]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth E] Focus chain X [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
P1L Query on P1L	E [auth C]	L-PEPTIDE LINKING	C₁₉ H₃₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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: 2025-07-02

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